Can't get you out of my head
by Linnzi
Summary: The events of The Hive have not left Lt. Col. Sheppard untouched. As the team worries for his mental health, Sheppard becomes obsessed with finding his former lieutenant, Aiden Ford...COMPLETE.
1. Chapter 1

Can't get you out of my head. 

_This is for Shelly, who wanted me to write a tag to the Hive. Thanks to Merlin and Kodiak, my trusty betas, for their input and advice. As usual, all mistakes are my own._

_I don't own Stargate Atlantis or its characters etc..._

Chapter 1.

Sheppard quickly slipped away from the infirmary, hoping to avoid his post mission check. As he quietly exited, he couldn't help thinking how fortunate they'd all been.

McKay, Teyla and Ronon were fine, and were recovering well from the effects of the Wraith enzyme. All things considered, they had gotten off lightly. McKay had escaped the clutches of Ford's cronies, and Sheppard had escaped the Hive with Ronon and Teyla, via the dart. The Hive ship had conveniently been destroyed in the process of destroying another Hive. They'd been lucky, _this_ time, and were safe back home in Atlantis. Well, except for Ford. _Ford._ Sheppard's heart sank when he thought of the kid. Yet again, he'd let his former second in command down. Instead of helping him escape, bringing him back to Beckett for help, he'd agreed for him to watch their backs and he hadn't seen him since. Had he escaped the Hive? Sheppard thought he had. Hoped he had. _Another time, another place, Ford, _he thought.

"Colonel?" Beckett's voice interrupted Sheppard's surreptitious escape.

Sheppard turned to look at the doctor, smiling. "Doc. What can I do for you?"

The colonel saw the look on Beckett's face, and inwardly groaned, knowing what was coming. "It's more a matter of what I can do for you, I think," Beckett answered matter-of-factly. "In there. Now!" Beckett had suddenly switched from his usual soft Scottish lilt to one of his 'don't mess with me, Colonel' voices. Sheppard knew better than to disobey Beckett when he used that tone. _Mild-mannered Scot, my ass_, he thought to himself.

"Okay. I'm going!" Sheppard answered, inwardly cursing himself for not being stealthier.

Beckett followed the colonel back into the infirmary, and pointed to a bed. "Sit," he ordered.

"What am I, a dog?" Sheppard moaned, by way of reply.

The doctor snorted. "No, not a dog. You're not well trained enough for that. Right then. Post mission check. Anything unusual to report?" Beckett eyed Sheppard suspiciously, and the colonel knew it would be better, in the long run, to be honest.

"Ah, not really. Got stunned a couple of times. Ronon elbowed me in the face. Other than that, nothing comes to mind." Sheppard knew he wasn't being totally honest, but figured it was worth risking Beckett's wrath by not admitting to his encounter with the Wraith queen.

Sheppard watched Beckett, wincing as he saw the doctor plaster one of his 'I know you're lying' smiles on his face. "Really. Are you sure about that, Colonel?"

The colonel considered his options: be honest and spill the beans, or, continue to – _stretch_ the truth. He opted for the latter. "Nope. Just the usual." Sheppard smiled,what he thought washis most charming smile, as he watched Beckett start his usual battery of tests.

Beckett raised an eyebrow and sighed. "Right. So I must have misunderstood Teyla when she told me the Wraith queen interrogated you using telepathy, then?" Sheppard's smile instantly dissolved, and he thought about having a quiet word with the Athosian about what she should and shouldn't tell the doctor, in the future.

"Oh, that. Didn't think it was important. Nothing happened. She asked some questions, I…declined to answer them. She tried to get me to squeal by doing the old Jedi mind trick. It didn't work. That's it." Sheppard shrugged, really, it _wasn't_ a big deal. The fact that his head was beginning to pound and he wanted nothing more than to lie down was irrelevant, he decided.

Beckett tutted, "Not important?" he asked incredulously, as he walked over to a nearby shelf, retrieving something Sheppard couldn't identify, and walked back, arms out-stretched. "Scrubs. Get in them. Now."

"_Doc!"_ Sheppard pleaded, "I'm fine. Really. Do all the tests you want. I'll behave. But no scrubs…"

Beckett regarded his recalcitrant patient. "Stop whining, Colonel. You're sounding more like Rodney every day. Though he's not usually whining about leaving the infrimary or wearing scrubs. Quite the opposite, actually." Beckett gave Sheppard his no-nonsense smile, and continued, "Your blood pressure's a little high and I need to do some scans and get some blood work done, just to make sure everything's okay. It'll only take a few hours. So get changed, and I'll be back shortly." With that, he pulled the privacy curtain round Sheppard's bed and left the sulking man to change.

-oOo-

Five long and miserable hours later and Sheppard had finally been released from the infirmary, after much wheedling, whining and moaning. Beckett had let him go reluctantly, after having given him a clean bill of health. He knew he should obey Beckett's instructions to have something to eat and get some sleep, but needed to speak to Weir before the planned de-briefing, which was scheduled for the next morning. After shaving, showering and changing into clean clothes, he headed for the control room.

Entering the room he saw Weir was in her office and walked over, stopping in the doorway and leaning casually against the doorframe.

Elizabeth Weir looked up from her laptop and frowned at Sheppard. "I thought Beckett told you to get some sleep. Yes, before you start defending yourself, he told me he'd given you the all clear. He also told me you had a headache and needed to eat and rest. So, why are you here?"

Sheppard entered the small room and plopped himself lazily down on the chair opposite the doctor, slouching immediately. "Just wanted to catch up with you before tomorrow's briefing. I'll go and get some food in a minute, and then I'll get some sleep. For your information my headache is gone; Beckett gave me some Tylenol and it did the trick," he explained to Weir.

"Okay. I already know the basics of the last few days. What's on your mind, John?"

Sheppard knew the good doctor could see straight through him. "Ford," he answered solemnly.

Elizabeth Weir studied her military commander, and sighed. "I know you feel responsible for what happened. So let's end this right now. You couldn't have done anything more than you did. He put you all in danger, leaving you with no choice but to agree to the drugging of your team, and to participate in a fool-hardy raid on a Hive ship." Weir paused for thought, and stood, walking over to where Sheppard forlornly sat. "He's dead, John. Let's accept that and move on."

Sheppard looked up at Weir, shaking his head. "No, he's not. I know he managed to escape. I just…have a feeling. I want to look for him. I owe him that much. I want you to give me the go-ahead to mount a search for him." He looked up at Weir as she squeezed his shoulder with her hand.

"John, he's dead. I know it's hard to accept, but we must. Permission denied." She walked back behind her desk and sat down, grimly smiling at Sheppard, and asking, "Anything else?"

The colonel studied Weir for a moment, desperately trying to control the anger that suddenly was threatening to spill out of his lips. He took a deep breath. "Elizabeth. Listen to me. I know he's out there. We need to search any planets near to where the Hives were. He needs our help. I know he's behaved badly, but it's not his fault. You've seen first hand what the enzyme did to McKay. I can't just abandon Ford. Please, let me do this." He'd beg if it would make Weir change her mind.

Weir bit her lip, exhaling, and shook her head. "No, John. You don't even know he's alive. It's a waste of resources and time."

Sheppard stood, and started to pace. "A waste of resources? Is that what Ford is? A waste of our time? He's our friend, Elizabeth. He wouldn't even be in this mess if I hadn't woken up the Wraith. I… we owe it to him to help him. We don't leave people behind. Remember?" How could Elizabeth not want to find Ford? They had to help him. _He _had to help him.

Suddenly Sheppard felt himself sway a little as a sharp pain jabbed at his head. He reached out, placing a steadying hand on the nearby chair. '_Kneel', _suddenly echoed in his mind, and he felt his knees give way as his body obeyed the overwhelming desire to obey the internal command.

Weir immediately ran over, kneeling down, looking into his eyes in concern. "John? What's wrong. Do you want me to call Beckett?"

The pounding in Sheppard's head continued, the voice echoing relentlessly through his mind. "Stop…make it stop," was all he could grind out. Placing his head in his hands, Sheppard screwed his eyes shut, panting to try and relieve the hammer being rammed repeatedly into his skull. Weir gently placed her hand on his shoulder, and tapped her radio.

"Weir to Beckett. We have a medical emergency in my office," she called into her earpiece, as she tried to soothe Sheppard.

The colonel whimpered as the voice continued to haunt him, the pain in his head having escalated to knives being driven into his skull.

"Just…make it…stop…'Liz'beth…please…" Sheppard begged.

His plea was answered when he saw a white flash in front of his eyes as an agonising wave of pain drove into his head. Screaming, he flopped on the floor as his knees gave way, rolling onto his side into a foetal position. Another blinding flash, and he surrendered to blissful unconsciousness.

-oOo-

Beckett ran into the control room and headed straight to Dr. Weir's office at full pelt. Seeing Sheppard lying on the floor, with an anxious Dr Weir kneeling at his side, he stopped and silently cursed, knowing he should have kept Sheppard for observation in the infirmary. "Elizabeth. What happened?" he asked the obviously concerned woman.

Weir looked up at Beckett. "We were talking; he wanted to go looking for Ford. I told him he couldn't and he became agitated and then collapsed, asking me to 'make it stop'. I think his head was hurting him," she explained.

Beckett examined Sheppard and tapped his radio, calling for a gurney. He looked at Weir, muttering, "I knew I shouldn't have released him. Damn, why do I always let him get his own way?"

"Carson, is he okay? Do you know what's wrong?" Weir had already thought she'd lost her friend once today, and didn't want to contemplate losing him a second time.

The doctor grimaced, answering, "I haven't got a clue. His tests and scans were all clear. He's not responsive at the moment, but stable. Best I can do is get him settled in the infirmary and run some more tests."

Weir sighed, studying the unconscious man lying on her floor. "Carson…"

"Aye. I'll let you know, lass," he answered, not needing to know the question.

-oOo-

Consciousness returned to Sheppard slowly, and painfully. The first thing he was aware of was the pounding in his head. _Funny, I don't remember guzzling any of Radek's moonshine,_ he thought in his confusion. No, he hadn't been drinking, he remembered. So why was he feeling like hell? He tried to piece together his memories. Ford. The Hive ship. The Wraith queen. Suddenly his pain intensified, and he groaned as he remembered the sound of her hypnotic voice, commanding him to kneel. Feeling nauseous, he decided maybe keeping his eyes shut was the better option, but tried to think where he was. In the cell? Was that where he was? No, he was in a soft bed. He was in Atlantis.

Sheppard remembered talking, arguing, he corrected himself, with Elizabeth. Then the pain had hit - and the voice. _Her _voice. He was relieved to realise that there weren't any voices in his head now. Wouldn't Beckett just love that, the head of the military, hearing voices. If he admitted that to Beckett, he'd be given a one way ticket to see Heightmeyer, that much he knew. Finally, deciding to brave a quick peek of his surroundings, Sheppard opened his eyes to a slit. The pounding in his head intensified as he tried to focus on his surroundings. Groaning, he turned on his side, wincing as the pull of an IV in his hand told him that he was in the infirmary.

"Colonel. How are you feeling?" Beckett's voice filtered into his weary brain.

Groaning more, Sheppard whispered, "Like I stayed at the party way too long…"

Beckett chuckled, and started checking his patient's vitals. "Headache still bothering you? I'll get you something for that in a minute. Feel up to some breakfast?" he asked.

Sheppard groaned again. "Not unless you want it to make a re-appearance. Crap… what's wrong with me?"

The doctor sighed, as Sheppard slowly turned onto his back, eyes opening to slits as he tried to focus on Beckett's face. "To be honest, I'm not sure. Do you want to tell me what happened?"

The colonel sighed, answering, "I was talking to Elizabeth. My head started pounding, and I saw flashing lights. Then I just passed out, I think."

Beckett considered Sheppard's answer. "You're displaying the classic symptoms of a migraine, though that doesn't explain you losing consciousness. Your blood pressure is a little high, otherwise everything checked out fine."

"Never had a migraine before. Why now?" Sheppard was beginning to suspect his little Q and A with the queen might have had a bigger impact on him than he first thought.

Beckett considered the colonel's question before answering. "Migraine's, assuming that's what we're dealing with, can occur at any age and be triggered by many different things. I'll be honest with you, Colonel, there's a lot we don't know about them, though stress certainly can be an important factor. The last few days have been pretty rough for you, I'd guess. You've also been stunned twice, and being knocked around a bit could have contributed to this little…episode. Oh, and let's not forget your encounter with the Wraith queen."

Sheppard sighed. "Don't see what she's got to do with any of this, Doc." If he was going to be able to make an escape from the infirmary any time soon, Sheppard knew he'd have to play down the queen's little mental torture routine.

"You wouldn't. Bottom line, we have no idea what her probing of your mind and interrogation could have done, despite your scans all being clear. We simply have no other basis for comparison. Not many of my patients seem to survive getting close to Wraith queens." Beckett paused, before continuing, "Before you ask, you won't be leaving my care today, Colonel. Another twenty-four hours, for observation. I'll go and get you something for that headache now." Beckett smiled kindly and walked off, returning shortly with a syringe which was swiftly injected into Sheppard's IV port.

Beckett patted his patient on the arm. "That should make you feel a little more comfortable. I'd really like you to get some food in you, but I think you should try and get some sleep first. I'll send Shelly with a sandwich for you at lunchtime."

Sheppard inhaled sharply. "God, the briefing! I've missed it, haven't I?" He groaned inwardly. Caldwell would just love that. After the commander of the Daedalus' attempt to usurp Sheppard as head of the military in Atlantis at the time of the 'unfortunate retrovirus incident', as Beckett euphemistically referred to it, Sheppard knew Caldwell would be rubbing his hands in glee. Atlantis' military commander incapacitated – again! Great!

"I'm afraid so, Colonel. Dr. Weir said she'll go over things with you later, when you're feeling better. There's nothing to tell her that can't wait. Sleep. Now, if you need anything, just buzz." Beckett smiled, and walked away, leaving his patient to rest.

-oOo-

Rest did not come easily to Sheppard; neither did sleep. His head was still throbbing, though the meds Beckett had given him had somewhat dulled the pain. The colonel tossed and turned, finally drifting into a restless slumber.

_Sheppard saw Ford in front of him, calling to him, then screaming. The Wraith queen was standing in front of the former lieutenant, hand on his chest. Sheppard screamed for her to stop, raising his P90 and taking aim at the tall, white-haired creature. Sheppard heard Ford scream as the queen began to feed from him, and watched in horror as the young man began to age. I won't let this happen, not again. Sheppard steeled himself and fired the automatic weapon. The queen turned around and hissed, as Ford's lifeless body fell to the ground, his head a bloody mess where Sheppard's bullets had found their mark. _

'_Kneel' echoed in Sheppard's head, as his body yet again betrayed him, and he was forced to his knees. The Wraith queen towered above the colonel, and snarled as her hand slammed into his chest. Sheppard screamed as he felt his life drain away…_

Screaming, Sheppard woke up, bolting upright in bed, sweat dripping from his forehead. He gasped as the jackhammer in his head pounded away, and flopped back against his pillows, desperately trying to calm down. A dream, it was a dream. Sheppard knew that.

He felt a hand on his arm, and opened his eyes to see the pretty young nurse, Shelly standing over him. "Colonel? Are you alright?" she asked him in a concerned voice.

It took all of his will power to answer the nurse without whimpering. "Ah, bad dream. Sorry. I'm ok now." He mustered a half-smile and closed his eyes, praying Shelly wouldn't inform Beckett of his little outburst.

"Alright then. Can I get you anything?" the nurse politely questioned the colonel.

"No, no- I'm good."

The nurse returned to her duties, but Sheppard noticed as he opened his eyes that she turned around, her eyes lingering over him.

-oOo-

After a day in the infirmary, Sheppard was relieved that Beckett discharged him, as promised, on the proviso that he rested and only performed light duties. Sheppard was relieved to be free from the place he seemed to spend so much of his time; the infirmary was becoming a second home to him.

After de-briefing with Weir, and writing his mission report, Sheppard headed to the mess to try and get some food down. Beckett had continually been nagging him to gain some weight after the 'turning into the bug' episode. The doctor had threatened to force feed him on numerous occasions, to 'get some fat on your skinny arse' as the Scotsman had delicately put it.

Sheppard entered the mess, picking up some soup, Athosian bread and a glass of juice. As he made his way to a table, he noticed McKay waving at him, and walked over to the scientist, flopping down in the empty chair opposite. McKay eyed Sheppard suspiciously, asking, "You ok? Heard you fainted on Elizabeth last night."

"Funny. I don't faint, any more than you do. Beckett thinks I had a migraine. My head was killing me and I kinda saw flashing lights. I'm ok now." Sheppard thought it was prudent not to mention that the Wraith queen's voice had played a part in his collapse as well.

McKay grinned. "Good. I need you to come to my lab and touch something for me. You free?"

The colonel grimaced. "Is it urgent? I was going to lie down for a while…"

"It'll only take a few minutes. While we were… away, shall we say? Stackhouse's team found an artifact on L5B-196. It's Ancient, but so far no one has been able to activate it. As you're Mr Mega Gene, thought I'd ask you to give it a try." The scientist smiled at Sheppard, while his hands gesticulated wildly, as they usually did when McKay was being enthusiastic about some Ancient doodad or another.

Sheppard smiled, and nodded. "Sure. Why not? Beckett only okayed me for light duty anyway, so it's not as if I'm busy, or anything. Let's go." The colonel stood up to leave.

McKay frowned at his friend. "You haven't eaten anything yet. Don't you want to eat that?"

"Nah. Not really hungry. I'll get something later. Come on." With that, Sheppard picked up his tray, deposited it on the table where the used trays went, and headed out of the mess, McKay trailing behind.

McKay ran to catch up with Sheppard, and asked breathlessly, "You sure you're ok? You know, Carson will throw a fit if he finds out you skipped lunch. He's always complaining about how skinny you are…"

"Rodney, I'm fine. Headache's just made me feel a little nauseous. No big problem. I'll grab something later." Sheppard interrupted.

"Fine. Just don't go 'fainting' on me." McKay smirked, as he followed Sheppard towards the lab.

Once there, Sheppard sat on a stool, elbows on the workbench, waiting for the scientist to bring over his latest project. McKay almost skipped over to him, and held a small, cylindrical metal object for Sheppard to take. The colonel reached out to take the artifact, pausing before he touched it, to ask, "It's safe, right? Not going to explode or throw me across the room?"

"Honestly, I haven't got a clue," McKay answered as he gave his usual lopsided smile.

Sheppard raised his eyebrows. "McKay…" he started to say, but was interrupted by the sicentist.

"I'm sure it's absolutely safe. Now, just touch it, Sheppard."

Sheppard finally took hold of the Ancient cylinder, and thought 'on'. He felt warmth in the palms of his hands, and saw light emerge from under the device. He looked at McKay, and saw the smile on the scientist face. Sheppard was just thinking that McKay looked like a little boy first seeing his presents on Christmas morning, when he felt a jolt of white-hot pain stab across his forehead. "Ow!" he managed to cry out.

McKay's smile disappeared, as he asked in concern, "What's wrong?"

Sheppard looked at the scientist, and was about to explain, when the Wraith queen's voice returned with a vengeance. As '_kneel' _began to echo relentlessly in his mind, Sheppard once again felt agonising waves of pain run through his head. Flashes of white light erupted in front of his eyes, and he suddenly felt nauseous. Falling off the stool on to his knees, he dropped the device, his hands reaching for his head. "No… not again…" he managed to whisper.

McKay ran to Sheppard's side, and kneeling, questioned the colonel, "What? What's wrong?"

Sheppard tried to answer, but as the pounding increased, and the voice in his mind deafened him, he cried out. He felt bile rising in his oesophagus, and managed to plant his hands on the floor as he doubled over, violently vomiting.

"Jesus!" McKay exclaimed, while tapping his earpiece. "McKay to Beckett. I've got a medical emergency in my lab."

As he reached to support Sheppard, the colonel cried out again, then, as McKay gently lowered the prone man onto his side, McKay heard his friend whisper, "Get her out of my head…please. Just… make her stop…"

Sheppard looked up at McKay, and, as darkeness approached, distantly heard the echo of footsteps in the hall outside. Another stab of white-hot pain overwhelmed him, and he simply whispered, "M'Kay…I can't do this…not again… get her…out of my head."

McKay knelt in stunned silence as Sheppard stopped writhing and closed his eyes, finally succumbing to unconsciousness.

Tbc.


	2. Chapter 2

Chapter 2.

_Thanks to Merlin and Kodiak for their advice and beta skills. All mistakes are my own..._

"He said _what_?" Beckett's voice echoed around his office.

A nervously pacing McKay stopped and looked at Beckett. "He said 'make her stop' and 'get her out of my head'. Oh, and let's not forget, 'I can't do this again.'"

Beckett frowned, muttering something McKay couldn't quite hear; though the scientist recognised the annoyance displayed in Beckett's body language. "I knew he was keeping something from me! What is it with him? He can't just tell me what's going on, can he?" The doctor was somewhat pissed, McKay noticed. _Okay, make that really pissed,_ McKay corrected himself.

He interrupted Beckett, "Oh come on, Carson. Would you admit to thinking the Wraith queen was 'in your head'? I know I wouldn't." McKay paused, and looked Beckett in the eye. "So, with all those letters after your name, I'm sure you 'll be able to explain to me what the hell is wrong with him?"

Beckett sighed, massaging his forehead with his hand. "I have no idea what's going on. He's suffering migraine-like symptoms. His blood pressure is high, and his seratonin levels are a little up. Other than his brain activity being a little higher than normal, his tests have all come back completely normal."

"Well at least his little fainting spell had nothing to do with the artifact he was holding. Zelenka analysed the readings I took, and it's some sort of diagnostic tool, probably medical," McKay explained to Beckett.

The Scotsman's head jerked up, as he took in what the scientist had told him. "A diagnostic device? That could explain a lot. Perhaps it scanned his brain and triggered the 'episode' the colonel experienced. Can I see the readings from the device?"

McKay sighed, answering, "You can, but you won't understand them. I'll go over them and see if I can make heads or tails of anything there. Zelenka couldn't make sense of most of it, but then again, he's not me, is he?"

Beckett snorted. "No, he's not. Thank God. Let me know if you find anything of interest. I'll fill Elizabeth in on what's happened. She's in a meeting with Caldwell at the moment, and I thought it might be prudent to wait till he's gone before telling her about this."

Grinning, McKay couldn't help but quip, "Hah! Not only a voodoo expert, but a diplomat as well. I'm impressed, Carson."

The doctor raised his eyebrows. "Cheeky, Rodney. If I were you I'd go and analyse those readings before I use your bum as a pin cushion…"

Not needing to be told twice, McKay quickly moved, making a hasty exit from Beckett's office.

-oOo-

Waking up this time, Sheppard knew exactly where he was. Head throbbing, feeling nauseous and an IV line present in his other hand this time, he instantly knew he was in the infirmary – again. Gingerly opening his eyes, he concentrated on focusing at the figure sitting in a chair by his bed. Ah, Beckett, and looking none too pleased.

"Colonel. I see you've decided to join us. How are you feeling?" Beckett asked rather shortly.

Sheppard groaned. "Pretty much like last time Doc. How long have I been out?"

Beckett sighed, before answering, "About eight hours. Why didn't you tell me these headaches were linked to the Wraith queen's probing of your mind?"

_Straight to the point, Doc,_ Sheppard thought. "I don't know that they are. Why do you think that?" Sheppard had a horrible feeling he'd let something slip while he was not feeling himself.

"Rodney told me you said, 'get her out of my head' before you passed out," explained Beckett, and Sheppard could sense the doctor's annoyance.

_Great! _Sheppard thought to himself, _how do I get out of this one?_ "I don't remember saying that. Perhaps McKay mis-heard. I'm not hearing voices, Doc."

Beckett gave a sad smile. "I didn't say you were. Strange you believed I thought that though. Are you?"

"Am I what?" Sheppard sighed. He wasn't deliberately being obtuse, he reasoned. No, that was a lie, he was, if he were being honest , but he really didn't want Beckett finding out that quite possibly he was going, what was the word? Oh yes, _nuts._

"Don't play games with me, Colonel. Are you hearing the Wraith queen's voice in your head, or not?" Beckett was in no mood for his attempt at deflecting questions, Sheppard could see.

"No." It was simple to lie. God knows, he'd done it enough times. Sheppard actually didn't enjoy being deceitful, but knew that admitting to hearing voices would be a bad career move, especially with Caldwell waiting in the wings, ready to pounce. It also wouldn't help in his search for Ford

Beckett looked directly at Sheppard, making the colonel shrink back into his bed, before simply saying, "I see. If you don't tell me what's going on, I can't help you, lad."

Sheppard, sank further into his pillows, closing his eyes briefly, in thought. "I'm telling you all I can, Doc." That wasn't a lie, Sheppard reasoned. He _couldn't _tell Beckett everything. Not if it meant losing his job, and being put in a straight jacket.

Beckett patted Sheppard on the arm, smiling as he stood. "Try and get some rest. How's the headache?"

"It's bearable. Doc?" Sheppard paused, biting his lower lip, before continuing, "I'm…look, I don't mean to be a pain in the ass. I'm sorry. Thanks for taking care of me."

"Just get better, Colonel. Then I'll be happy." Beckett started to walk away, but turned back to look at Sheppard. "And…you're welcome."

Sheppard settled back in his pillows, closing his eyes, and praying the Wraith queen wouldn't disturb his dreams again.

-oOo-

After another twenty-four hours of observation in the infirmary, Sheppard was relieved to be released. Beckett had for the second time in as many days, reluctantly released Sheppard and allowed him to return to light duty, along as he promised to get plenty of rest. Sheppard's headache had been reduced to a dull throb, though he knew that was because of the meds Beckett had given him. Frustrated at being limited to Atlantis, and light duty, Sheppard figured if he behaved himself, that he'd be cleared for full duty in a day or so. In the meantime, he had decided to spend his enforced down time researching the planets near to where he last saw Ford. If Elizabeth wouldn't let him search for Ford, he would use all the available resources to find him alone. He owed his former second in command that much.

Walking towards one of the research labs, Sheppard was surprised when Caldwell passed by, stopping to talk to him.

"Colonel. How are you feeling - better, I hope?" the senior officer asked.

Sheppard plastered on his best smile. "Yes, sir. I'm good."

Sheppard could tell Caldwell was scrutinising his face, and the pilot just knew Caldwell wouldn't leave things at that.

"Dr. Weir tells me you've become somewhat obsessed with finding Lt. Ford. I hope it's not necessary for me to remind you that it is your duty to set an example to those under your command?"

"No, sir." Sheppard felt the anger in him escalate as the colonel riled him. Why would Elizabeth tell Caldwell something like that? They were supposed to be a united front against the commander of the Daedalus, and Sheppard was surprised at how betrayed he felt; the fact that Elizabeth would speak to Caldwell about him in confidence like that smarted.

Continuing, Caldwell smirked, "I really am not surprised, Sheppard. Your instincts and emotions drive you. If you think I'm going to stand by and watch you erode the morale among the military personnel here – think again. Pull yourself together. If I thought Ford was alive, I'd be searching for him using the Daedalus' sensors. He's a security risk and _I _wouldn't hesitate to eliminate him, if the opportunity arose…"

Sheppard blanched at the colonel's words, anger threatening to boil over. He interrupted Caldwell, "With all due respect, sir. You don't know Ford, or what he's become. He's very resourceful, and it would be foolish to underestimate him."

Caldwell balked at Sheppard's words. "It would also be foolish to continue searching for a dead man when you have been ordered not to, Colonel. It would be a shame if I were forced to report to Stargate Command that I am concerned about the ability of the military commander of Atlantis to perform his duties." Caldwell paused, and Sheppard inwardly flinched at the venom in the man's voice. "I suggest you get some sleep and think carefully about what you want. Just because Dr. Weir has the President's ear, doesn't mean she has carte blanche over everything that concerns the military. You'd do well to remember that, Colonel."

Sheppard watched as Caldwell strode off down the corridor, suddenly feeling pain from the unconscious clenching of his hands. He headed determinedly towards the lab, seething with anger, head pounding furiously in time with his pulse.

-oOo-

As he sat hunched over a laptop in one of the research labs, Sheppard didn't notice McKay enter, and stealthily approach him. He was uncharacteristically taken aback when McKay suddenly started speaking.

"What exactly are you doing, Colonel?"

McKay's voice, catching Sheppard off guard, caused the pilot to jerk his head up from the laptop sharply, and Sheppard was shocked by his own complacency. He answered the scientist a little more sharply than he intended.

"Nothing. Nothing important. What are you doing here, Rodney?"

"I just asked you the same thing. I thought you were supposed to be taking it easy. It's late, you should be sleeping in your quarters. So, why are you here?" Sheppard could sense that McKay was suspicious.

"You wouldn't understand."

McKay studied Sheppard's face, and Sheppard noticed the worried look on the scientist's face. "Try me," McKay answered simply.

Sheppard let out a deep breath, massaging his aching neck. "Fine. I'm searching the database for the addresses to any planets near where the Hives were destroyed."

"Why would you want to do that?" McKay wearily asked. Sheppard noticed the scientist's head jerk, as if suddenly joining the dots together. McKay groaned, simply saying, "Ford. You want to find Ford. Jesus, Sheppard. He's dead. Why are you doing this to yourself?"

Sheppard clenched his jaw, trying to quell the anger coursing through his body. "I'm not doing anything to myself. I have to find him. He's out there, and I need to help him. Why doesn't anybody understand?" He let his head fall into his hands and sighed.

"What's to understand? He's gone. Even if he were alive, do you really think you could persuade him to come back here? In case you didn't notice, he likes being hyped up on the enzyme. He doesn't want to be helped. Hell, he doesn't even think he needs help. He thinks he's superman." McKay paused, making Sheppard look up at the scientist's face. "Sheppard, listen. I know how responsible you feel for Ford. What happened to him was …" McKay seemed to be searching for the right word, Sheppard thought. "It was…horrible. Okay? He didn't deserve it. But you punishing yourself by feeling unnecessary guilt is going to make you sick. So, just let this go. If, by some miracle he did survive, we'll run into him sooner or later. Come on, leave that, and let's go and get you some food, then get you to your quarters for some sleep."

McKay placed a hand on Sheppard's arm, making Sheppard jerk away sharply from the contact. Angrily he shrugged the scientist's arm away, shouting, "Just leave me the hell alone! If you don't want to help me, then… just go. I have work to do."

Sheppard raised a hand to his forehead, kneading his head, as the ever-present headache started to viciously throb.

"Fine. Be stupid. Make yourself sick. Carry on like this and you'll be relieved of duty, and then you'll be in Heightmeyer's clutches. Don't expect any sympathy from me." McKay turned to leave, and Sheppard saw pain in the man's face. "Sheppard? Please let this go. Get some rest and get better. I really don't want Caldwell running the military, not when I've already spent so much time breaking you in." McKay smiled half-heartedly, and Sheppard felt a pang of remorse.

"Look, I appreciate what you're saying, but I have to do this. Really. Once I find Ford everything will be fine. Okay?" Sheppard lowered his head and continued scrolling through the database, distantly aware of McKay leaving. _I will find him. Then we'll see who's being stupid, _he thought.The pounding in his head was starting to overwhelm him and Sheppard lowered his head onto the desk, shutting his eyes, as the Wraith queen's hypnotic voice reverberated through his skull once more. As she commanded him to kneel, this time he inwardly refused to obey, instead opting to be pulled into the soothing darkness of unconsciousness.

-oOo-

In the distance Sheppard heard someone calling his name. He couldn't make out whose voice it was. It sounded like… Ford. God, Ford. He needed help. He needed Sheppard's help. Trying to open heavy eyes, Sheppard realised he was crumpled in a heap on the floor of the lab. Groaning, he rolled over onto his back and squinted at the shadow looming above him. "Colonel? Are you alright? You want me to call Doctor Beckett?" Zelenka. It was Radek.

"Ah, no. I'm fine thanks, Radek. Must have fallen asleep." Sheppard slowly started to sit up, rubbing the back of his neck as the stiffness from sleeping on the floor made itself known.

Thinking he'd been lucky that it was Zelenka who had discovered him, Sheppard quickly got to his feet, wavering as he did so. Zelenka put out a steadying hand to help the colonel, just as McKay blustered in. Taking in the situation, Sheppard watched as McKay strode purposefully across the room, and stood in front of him, hands on hips.

Sheppard inwardly groaned, knowing what was coming.

"What the hell are you still doing here? Have you gone totally insane? No, don't answer that, because I already know the answer. You look like shit, Sheppard. Aren't you due to have a check-up with Carson this morning?"

Groaning, yet again, Sheppard looked at his watch, and noticing the time, ran a hand through his unruly hair. "Crap. He's going to kill me. I'd better go and shower. Thanks Radek." After smiling reassuringly at the two scientists, Sheppard practically ran from the lab, realising he had better get a move on, or his ass would be Beckett's.

-oOo-

How he got through his check with Beckett, Sheppard would never know. He looked like hell, and felt like it. Beckett was uncharacteristically subdued throughout the various procedures, and only asked Sheppard a few general questions.

Beckett refusing to return him to active duty wasn't a surprise, but Sheppard reasoned that it would actually give him more time to search the database and give him extra time to find ways of persuading Elizabeth to let him search for Ford. He had already identified two nearby planets, and was hoping he'd be able to charm Elizabeth into letting him go search them.

Walking to the mess to get some breakfast, for once following Beckett's orders, he was interrupted by a call on the p.a. system, asking him to report to Weir's office. _Well, I did try to get breakfast, _he thought, inwardly laughing.

On approaching Weir's office, Sheppard was unpleasantly surprised to see Beckett, Heightmeyer and McKay all squatting in various couches and chairs inside. He strode up to the door, pausing in the doorway, as Weir cleared her throat on seeing him approach.

"Come and sit down, John." She sternly said as the doors slid shut behind him.

Sheppard flopped on the nearest couch, and decided it was best not to say anything until Weir had spoken.

"I have asked Dr. Heightmeyer to be present at this meeting on Dr. Beckett's advice. To put it simply, we're worried about you, John. Rodney told me you slept in one of the labs last night, after he found you searching the database for planets that you believe Ford may be on."

Sheppard listened to Weir's words feeling numb, hoping his expression mirrored that feeling. He looked at Weir, and wondered what was coming next. He inwardly flinched as Weir continued. "You obviously are not feeling very well, and Carson has explained that you are still suffering headaches, nausea and certain other symptoms. I've called you here to discuss a plan of action. To be blunt, this can't go on."

Sheppard saw Weir falter, and her shoulders sag as she again paused. Composing herself almost immediately, she resumed her monologue. "I need you, John. Atlantis needs you. I don't know what's going on, but something is very wrong with you, and I need to find out what it is. I don't want to ground you permanantly, but you're giving me little choice. What's happening?"

Feeling emotion well up, Sheppard bit his lip, before answering, "I just need to find Ford. But you won't let me do it, will you?" Sheppard paused, desperately trying to compose himself. When he felt himself calming down, he continued, "I'm not feeling great, you're right. I'm frustrated and angry, and I don't understand why you won't let me do such a simple thing. I'm not asking you for much. I just want to look for a friend who needs help…"

Sheppard again paused as his head started to pound again. He put a hand to his forehead, trying to ease the throbbing pain. Sensing everyone was staring at him, he lowered his hand, standing, before continuing, his anger no longer contained. "But the great almighty leader of Atlantis thinks it's a waste of resources, a waste of time. How the hell do you think I feel when you say things like that? You even spoke to Caldwell about me. I thought I knew you, thought you understood me. Now I don't know what to believe anymore…" Sheppard started to pace up and down, kneading his forehead with his hands again.

Weir sighed, and Sheppard saw her start to stand, but a firm hand from Dr. Heightmeyer stopped her in her tracks as the psychologist calmly stood up, and walked over to Sheppard. "Colonel, I think you should sit down. Whatever is upsetting you, we can talk about it together. Quietly and calmly. There's no need to get upset."

"Really? Oh I see. You think I'm losing it, don't you? What? I'm not allowed to have emotions and care about somebody? How can I talk about this calmly, when I'm told my friend is not important and is a waste of time? I just want to look for him, that's all. Why is that so difficult to understand?"

Sheppard abruptly stopped, the pain in his head rising to a crescendo.

"I…I don't understand you…any of you. Ford is just a kid…who needs help. Why… won't you let me find him?" Sheppard fell to his knees abruptly as the Wraith queen's voice again echoed in his mind. "God… no. Not again…please." As his interrogation with the queen replayed in his mind, Sheppard managed to grind out, "No…I'm not going to tell you…I'm not going to kneel…Stop…just stop!"

Beckett suddenly appeared above Sheppard, and gently unzipped his black shirt, pulling aside the fabric to expose his upper arm.

Sheppard jerked in surprise. "What… are you doing? No…leave me alone!" He cried out, trying to wriggle away from the doctor.

As he felt a prick in his shoulder, he looked at Beckett, and heard him whisper, "I'm sorry, lad."

Feeling himself gently being lowered to the floor, Sheppard was aware of a fuzzy, warm feeling enveloping him and he felt himself falling into darkness yet again.

Tbc.


	3. Chapter 3

Chapter 3.

_Thanks so much for the reviews! I owe a huge debt of gratitude to my betas, Merlin and Kodiak, for keeping me on the striaght and narrow. This chapter has spoilers from certain season 1 episodes as well as season 2. All mistakes are my own._

"What the hell is wrong with him, Carson?" McKay paced back and forwards in Beckett's office, nervously wringing his hands together.

Beckett sighed, looking at McKay. "Come and sit down, Rodney." Beckett looked over at Dr.Heightmeyer. "Kate, perhaps it would be best if you explain to Elizabeth and Rodney what we think is happening?"

Dr.Heightmeyer nodded in agreement. "We believe Colonel Sheppard is showing signs of a possible mental breakdown. The headaches, irritability, obsessional behaviour and aggression all are classic symptoms of him not being able to cope with events that have occurred recently…"

"You mean he's going nuts?" McKay interrupted.

Dr. Heightmeyer smiled patiently, before answering the scientist, "No, Rodney. I mean his mind can't cope with the trauma he's experienced. I believe the guilt of losing Ford and, in fact, many men under his command, has weighed far more heavily on him than we have realised. Combined with the burden of command and the physical stress of being interrogated by the Wraith queen as well as other physical hardships, put quite simply – his brain has had enough."

Weir grimaced. "So, you're saying the stress he's experienced has been building up, and now he's reached overload?"

Heightmeyer considered Weir's words. "Yes. That's a real possibility. The colonel is a very private person. He doesn't share his feelings easily. He internalises everything, while outwardly appearing strong. Underneath this strong exterior we don't know what he's feeling. He doesn't want us to. In previous sessions we've had together he is very guarded in what he reveals. He is always trying to deflect my questions with humour, or throwing questions back at me, yet always in a polite and charming manner."

The psychologist paused, smiling, before continuing, "Colonel Sheppard is unusually intelligent. I'm sure you all know his IQ is extremely high. He is very adept at evading my questions. From reading his past psychological evaluations I can tell you he has got it down to a fine art." Heightmeyer paused again, taking a breath before starting up again. "I believe recent events have pushed him too far, and the physical symptoms he's been suffering are a manifestation of his mental breakdown."

Weir nodded. "Okay. He's stressed, he's behaving out of character and it's making him sick. What do we do about it?"

Beckett sighed, before answering, "There are various therapies we can try. Medication can help. Obviously, talking to Kate is a must. The colonel needs to admit what he's feeling and talking about it will definitely help. However, knowing him, this will not be easy. He's not comfortable talking to psychologists, so you two," Beckett gestured towards McKay and Weir, "being closest to him, may be able to help."

McKay balked at Beckett's words. "Ah, yes. Not my strong point, Carson. Personal relationships, that is. Though obviously, I won't let him down. I'm here if he needs me."

Weir nodded. "Me too, Carson. What ever he needs, we'll be here. How long before he shows improvement? He is going to get better, isn't he?"

Heightmeyer smiled gravely, and answered the question for Beckett. "I see no reason why he shouldn't recover…eventually. If this is a stressed induced episode."

McKay and Weir looked at each other nervously. "Ok, what do you mean by 'eventually'? And '_if_' it's stress induced? What the hell does that mean?" McKay asked, anxiously.

"Rodney, there are no magic figures I can quote you. The human mind is very complicated. The fact that he has been hearing voices and having nightmares is quite worrying. There could be any number of psychological illnesses he is suffering from, and it's going to take time to rule out certain serious ones," Heightmeyer replied.

"Hang on a minute. You don't think he's showing signs of something like schizophrenia, do you?" McKay suddenly became noticeably concerned, the pitch of his voice raising.

Heightmeyer frowned. "It's also a possibility. I can't rule anything out at this stage. I think it's unlikely though. Post traumatic stress disorder is another strong possibility. It's just too early to tell."

Weir's hands wearily rubbed her tired eyes. "Ok. This is more serious than I thought. Are you sure there is nothing physical causing his problems? The Wraith queen did interrogate him, and he was fine before that…"

Beckett interrupted Weir. "It's unlikely, Elizabeth. Every test I've run has come back negative, every scan clear. His seratonin levels are still a little high, but not seriously so. I can't find any physical reason for the headaches, voices or his recent behaviour. Therefore I must assume it's a psychological problem."

McKay snorted. "Oh, that's just brilliant! You can't find anything physically wrong, therefore he's nuts. Typical doctor conclusion. Now you see why medicine is not a science, Elizabeth?"

"Rodney, you're not helping," Weir solemnly warned McKay.

Beckett grimaced. "I know you're worried, Rodney. So I'll ignore that remark." The doctor smiled at Weir and McKay. "Let's not write him off yet. He's a very strong man, and I'm hopeful this is just a hiccup. When he wakes up and we can start talking to him, we'll have a better idea what's going on. As he's sedated he won't be waking up anytime soon, so I suggest we all get some rest. If anything happens, I'll call you immediately."

Weir and McKay nodded, both standing and exiting the small office. Weir put a comforting hand on McKay's arm. "He'll get through this. He's too strong not to."

McKay looked Weir in the eye. "I hope you're right, Elizabeth. I hope you're right."

-oOo-

Sheppard woke up feeling disoriented, foggy-headed and nauseous. His head felt a little better, though his mouth was dry, feeling as if it were stuffed full of cotton wool. Yet again, an IV was stuck in him, this time in his inner forearm.

Opening his eyes experimentally, he was surprised to discover he was alone, and as the lights in the infirmary were dim, that it was night.

Slowly sitting up, Sheppard thought two things. Firstly, that he needed to get out of the infirmary, and secondly, he was in deep trouble. The former problem he could do nothing about until Beckett discharged him. Trying to escape would only make matters worse. The latter was a huge problem. He accepted that Beckett and the others now knew about the Wraith queen's visits in his head, and probably thought he was insane.

Sheppard's musings were interrupted when Beckett walked in, smiling.

"Colonel? Glad to see you're awake. How are you feeling?"

"Better, thanks. Look…" Sheppard struggled to find the right words. "I'm sorry about earlier. I wasn't feeling myself and said a lot of things I shouldn't have. These damn headaches are killing me, and I can't think straight. I should've told you about the Wraith queen paying me a visit or two. I was scared you'd think I was…not in complete control of my faculties, if you know what I mean?"

Beckett smiled. "You couldn't help it lad, I know that. You should have been honest with me, though I do understand why you were reluctant to share your little secret. We need to talk, Colonel." Beckett's tone suddenly became serious.

Sheppard nodded. "I know. Listen, I'm not going nuts. I know you think I'm obsessed with finding Ford, but he's alive. Trust me. I have to find him…help him. I shouldn't have lost it with Elizabeth, but I was so pissed that she'd talked to Caldwell about me. That hurt, you know?"

"I know. She only did what she thought was best, lad. She was worried. Your behaviour has been, well, let's just say you've been behaving a little out of character recently. I want you to talk to Dr.Heightmeyer."

Beckett looked at Sheppard, and grimaced. "Before you complain, if you want to be put on active duty again any time soon, you're going to have to. You need help. You need to talk about what's going on in that head of yours, and you need to start right away. You can also talk to Elizabeth and Rodney, they're very concerned and they are your friends."

Sheppard answered immediately, "Okay." He smiled at the shock he saw on Beckett's face. "What? You think I want to be plagued by headaches and feel like crap all the time? I'll do whatever you want. I just want to get better."

Beckett patted Sheppard on the arm, and grinnned. "Good. I've already scheduled an appointment with Kate for tomorrow morning. Try and get some more sleep. How's the headache?"

"Still there, Doc. But I'll live," Sheppard answered honestly. He knew he had to convince Beckett he wanted to get help, and that he recognised he needed it. If he could get these headaches under control, then get back on active duty, he could continue his search for Ford. That was his priority now. Sheppard settled down in his pillows, knowing tomorrow was going to be a difficult day.

-oOo-

_He was on the Hive ship, on his knees. The Wraith queen towering above him, as she ran a finger down the side of his cheek. Snarling, she taunted him. 'I will savour the taste of your defiance. Your friend was a coward. You, I will enjoy devouring.' He turned his head to look on the floor, and felt sick to see the dried husk of a man lying there. Ford, it was Ford. He screamed at his own impotence, the inevitability of his certain demise and at the injustice of it all. He screamed until his throat was raw, and gasped as he felt the dagger in his chest, as the life was slowly drained from his body…_

Screaming, Sheppard jumped out of bed, clambered over the rail in panic, landing on the floor with a thump. His heart felt as though it was going to burst through his chest, sweat dripped down his back, and it was all he could do to stifle a sob. As adrenaline pumped through his body, Sheppard was aware of someone calling his name.

"Colonel. It's alright, lad. It was just a dream. Try and take a few deep breaths…yes, that's it." Beckett – it was Carson standing over him.

Sheppard gulped, and suddenly became aware that he was shaking, and – crying? Men didn't cry, was all Sheppard could think. Big, bad, macho airforce pilots _didn't _sob because they'd had a bad dream.

"Sorry," he managed to whisper hoarsely.

Carson sighed. "It's okay, lad. Let's see if we can get you back into bed. Can you stand?" the doctor asked kindly.

"Yeah. Sorry, Doc. God, what the hell is wrong with me?" Sheppard ground out, while furiously wiping his tear stained face.

After getting situated comfortably back in bed again, Sheppard was aware of Beckett gently cursing.

"Ah, Colonel, you've ripped out your IV, and you're dripping blood all over your sheets! Never mind, you've soaked your bed with sweat anyway. Let's tape up your arm, change your sheets, and we'll get you some fresh scrubs. Then you'll feel much better."

Just as the doctor had uttered those words, Sheppard's body decided to thoroughly disagree with Beckett. As bile rose in the back of his throat Sheppard managed to lunge towards the opposite side of the bed, and hung his head over the rail, retching and gagging as he vomited bile over the floor.

Sheppard was aware of Beckett calling for help, and slumped back down into his cold, damp pillows, before managing to grind out, "Sorry, again."

"It's okay, son. We'll sort you out. Just try and calm down. We'll get you cleaned up, and then I'll give you something to help you sleep."

Sheppard looked up at Beckett through heavy lidded eyes, and before the approaching darkness claimed him, whispered, "I don't think I'll be needing anything to help with that."

-oOo-

Sheppard sat up in bed, anxiously waiting for Dr. Heightmeyer to arrive. His dream last night had left him feeling weak and vulnerable, as well as humiliated. Beckett had popped in to see him briefly that morning, and though Sheppard had apologised for his embarrassing outburst, and Beckett had reassured him not to worry about it, he still felt raw and spent.

He really didn't like psychologists, though Kate was a decent enough one, and a good person; pretty, personable and certainly not as bad as some shrinks he'd seen over the years.

"Colonel Sheppard. How are you feeling this morning?" Heightmeyer's voice brought Sheppard out of his reverie.

"I've been better." Sheppard grimaced, wishing fervently that he were somewhere else.

Heightmeyer smiled as she sat down in a chair next to the colonel's bed.

"I know. Carson told me about your dream last night. You know why I'm here, Colonel. We need to talk about what's been happening to you recently. I think your dream is a good place to start," the psychologist began.

"I'd rather not talk about it." Sheppard testily answered.

Heightmeyer smiled. "We don't have to if you feel uncomfortable about it. But it would help me to understand what you're going through."

Sheppard groaned. "Fine. It started out with what actually happened to me on the Hive. I was on my knees; the queen was in my head, forcing me to kneel. She ran a finger down the side of my face, one of those metal clawed ones. She told me she was looking forward to feeding from me, but then suddenly Ford was there, and he was dead, sucked dry, and I screamed, and then she started to feed on me. The pain was…so real. It was agony…" Sheppard paused and let out a shaky breath. "Sorry. Then I woke up. I'm sure Beckett's filled you in on the rest of my thrilling little performance?"

Heightmeyer nodded seriously. "He did. Though I don't think he found what happened to you entertaining in any way, Colonel. He was actually quite upset about last nights events."

"Sorry, Doc. I didn't mean to imply he did. I'm feeling pretty humiliated at the moment." Sheppard exhaled and tiredly rubbed the back of his neck with his left hand, wincing as he remembered the IV was now in his other arm after his little stunt last night.

"Do you often dream about Lt.Ford and the Wraith queen?"

"Yes," Sheppard quickly answered.

Heightmeyer nodded. "Okay. We need to find out why this has been happening."

Sheppard laughed bitterly. "You mean you need to try and work out why you think I've gone nuts. I'll save you some time, Doctor. I'm not insane, mentally ill, deranged or obsessed. Yes, I've heard the Wraith queen's voice. No, I don't know why. She's not been telling me to murder you all, or anything. I just keep replaying our little Q and A session over and over in my head," Sheppard paused, smiling insincerely at Heightmeyer.

"I have been suffering what Beckett thinks, are migraines. They've made me feel sick and tired. I can't deny that I've been…grumpy, and… less tolerant than usual. What can I say? McKay's obviously rubbing off on me." Sheppard plastered his best smile on his face yet again. He was going to keep smiling, until it worked or his face cracked, whichever came first.

Heightmeyer smiled back at the colonel. "I don't think you're 'nuts', Colonel. I believe that you may suffering from stress. That's what I'm here to determine, and hopefully to treat. Sometimes the mind can't cope with the events forced upon it, and the only way that it can tell you it's not coping, is to have physical symptoms manifest in your body. The headaches, dreams and voices you've been hearing certainly could be a result of that. Tell me about Lt. Ford. Why do you feel so responsible for the situation he's in?"

Sheppard briefly flinched, before composing himself. "Ford is…was, under my command. Of course I'm responsible for him. I let him down."

"How did you let him down?"

"I…I should have stopped him from escaping Atlantis after the Wraith attacked. I could have done more, talked to him, made him listen to me. I should have stopped him from diving into the Wraith beam when we found him on 'radiation planet'. That's what he would have named it, 'radiation planet'. He always gave the worlds we visited names. Used to drive me nuts. Now I miss that a lot…" Sheppard paused, his voice having grown gruff as his emotions overwhelmed him,

"It's perfectly normal to miss a colleague or friend, especially in circumstances such as those surrounding Lt. Ford's enforced absence. You weren't responsible for that, regardless of how you feel."

Sheppard listened to Heightmeyer's words knowing what she said made sense, yet not believing for a minute that her words were true.

After a brief pause, where Sheppard was aware of Heightmeyer's scrutiny, the psychologist continued.

"You feel responsible for the lieutenant's departure, yet realistically you couldn't have done anything to prevent his addiction to the Wraith enzyme or stop him escaping from you. Why do you think you blame yourself for his situation?"

Sheppard answered Heightmeyer's question with ease, though he was surprised by his honesty. "I woke up the Wraith."

Heightmeyer wrote something down on her palm pilot, Sheppard noticed. She then looked up at him.

"You didn't purposely wake the Wraith. You picked up a locket, and your gene activated a beacon, which alerted the Wraith. How is that your fault?" she earnestly asked.

"What does it matter? I still activated it. If I hadn't been on this mission, it wouldn't have happened. The Pegasus Galaxy would have been relatively free of the Wraith for another fifty years. How do you think that makes me feel?" Sheppard cried out, frustrated by his frailty and stupidity at letting Heightmeyer make him reveal things he wanted to keep buried.

Heightmeyer sighed. "Colonel, the Wraith would have woken up. What difference does it make that it was earlier than it should have been? You not being here would have been worse. Think of all the positive things you've brought to this mission."

Sheppard laughed. "Yeah. Like killing my CO? That was a positive contribution, wasn't it? What about pissing off the Genii, and then killing sixty of their men? That was one of my better efforts, wasn't it? Not to mention helping a load of convicts escape being lunch for the Wraith, and because of that innocent people were culled. Oh, yeah, I'm sure everybody is delighted I came to the Pegasus Galaxy."

Sheppard shakily took in a breath, desperately trying to calm down. His head had started to pound, and he suddenly felt the beginnings of a migraine starting up again. "Sorry, I need to lie down," he managed to grind out.

Heightmeyer put a hand on his arm. "It's alright, Colonel. Try and clam down. I'll get Dr. Beckett."

A few minutes later, Sheppard was aware of Beckett standing over him, he felt Beckett tugging at his IV, and suddenly felt a fuzzy warmth coursing through his veins. As the Wraith queen again entered his mind, he drifted off into drug induced sleep.

-oOo-

"Colonel Sheppard was unusually forthcoming in our session, and I feel we made a lot of progress. I'm optimistic that stress is the source of his problems, and nothing more serious." Heightmeyer looked at the three other people in the infirmary with her, before continuing.

"He is carrying so much guilt. I blame myself partly for not seeing this sooner. His charm, wit and intelligence can easily blind us, and we never see what's underneath his confidant and appealing exterior. So much has happened to him, none of it his fault, yet he blames himself for everything. I'm not sure there's anything we can do to make him change his mind about his role in events here. But, I believe discussing it, and getting him to admit how he felt, is the first step to his recovery."

Beckett was the first to respond to Heightmeyer's words. "That's encouraging news, Kate. You agree there's no need to medicate him at this stage?" Heightmeyer nodded her agreement. "Good. Obviously I'm giving him painkillers for the migraines. But I believe, in time, these will diminish, along with the replaying of his interrogation with the Wraith queen in his mind and his nightmares. In a way, this is like a mild form of PTSD. So, all things considered, I think he's turned the corner. Admitting those feelings will definitely unburden him, to a certain extent. Though obvoiusly this is just the beginning."

McKay snorted. "Sheppard just doesn't strike me as somebody who'd crack under the pressure. It's not him. You sure there's nothing physically wrong with him?"

Beckett considered McKay's words. "I'm pretty certain, Rodney. Sometimes these things can affect the most unlikely people. He doesn't vent his emotions or wear his heart on his sleeve like some of us do, and that can be very unhealthy for the mind."

"True. Something just doesn't add up, that's all," McKay grouched.

Weir smiled at McKay. "I know what you mean, Rodney. However Carson and Kate are the professionals here, and we have to trust them. What happens next?"

Heightmeyer answered Weir's question. "We carry on with the sessions. I feel we've made a real breakthrough here. He's admitted his feelings for the first time. Now he just needs to come to terms with what's happened. It will take time, but I'm feeling pretty positive."

Beckett grinned. "Good. I'll let you know how he's doing later. I'm sure he'd like some visitor's when his headache has improved. I'll just go and check on him now." Beckett walked away towards the curtained off section of the infirmary, as Weir and McKay wandered away.

-oOo-

The next three days passed slowly for Sheppard. His continuing sessions with Heightmeyer appeared to leave the psychologist very pleased with herself, Sheppard thought. He'd been released from the infirmary the previous day, and was confined to his quarters to rest, only being allowed out for sessions with Heightmeyer, check ups with Beckett or to go the mess for food.

Sheppard was pleased Beckett and Heightmeyer appeared to believe he was improving; he was obviously saying and doing all the right things. Deep down, Sheppard knew the two medical professionals meant well, but neither understood what he was going through, or what he needed to do to get better. He needed to find Ford.

His headaches had not really improved, but the analgesics and medication Beckett had prescribed for the migraines were working well. Sheppard had managed to keep the pain at a tolerable level, certainly low enough to fool Beckett into believing that he wasn't really suffering any more. He had enough pills left to last him for the foreseeable future, if he took them sparingly.

The voice of the Wraith queen was ever present in Sheppard's head, but somehow, and he really didn't understand why or how, he was managing to control his reactions to it. Certainly, losing his temper or becoming agitated exacerbated the problem, he had come to realise. His nightmares still hounded him though.

Sleeping was the most difficult thing for Sheppard. He dreaded it, constantly dreaming of Ford, the Wraith queen, with her hypnotic voice in his head. Just a few more days and he'd be allowed back on light duty, and then a couple more and he figured Beckett would ok limited active duty. Then he'd be able to go off and find Ford, and his problems would all be solved.

A knock on the door of his quarters brought Sheppard back to reality. On opening the door, he spied an anxious McKay standing outside.

The scientist smiled. "Can I come in?"

Sheppard stood aside, gesturing with his hand. "Yeah, sure. You ok?"

McKay snorted. "I was going to ask you the same. You certainly look better."

"Yeah. I'm feeling better every day. What about you?"

"Ah, I'm fine. I, er, came to have a talk with you." McKay sat down in a chair by Sheppard's desk.

Sheppard inwardly chuckled. "Oh -kaay. What do you want to talk about?" He knew full well the scientist had been sent there to talk about his 'feelings' and a part of him knew how difficult this was for Rodney. The other part was as amused as hell, looking forward to seeing the scientist squirm with embarrassment.

"Well, I just wanted you to know that if you feel the need to…if you want to…if it helps for you to…" McKay paused, and Sheppard thought he looked like a small animal trapped in a corner, desperate to escape its predator's clutches. "Christ, this is so not my forte. What I'm trying to say is, that I count you as a friend, and if you need to talk to someone, well, I'm here." McKay nervously put his hand through his hair, and Sheppard inwardly laughed as he heard the scientist mutter, "I am so crap at this stuff. Why couldn't Elizabeth do this? She's much better at playing friendships than me."

Sheppard smiled. "Thanks, Rodney. If I need to talk to somebody, I know where to find you."

McKay exhaled, and Sheppard felt a little guilty for enjoying the show. "Good, good. Well, if you don't feel like unburdening yourself anytime soon, I have a load of work to do. I'm going to get started analysing the readings on that artifact you touched the other day. As usual Zelenka has not been able to find out anymore. Sometimes to get things done properly you just have to do them yourself. Actually, I _always_ have to do things myself, but I digress. I'll stop by later and we can get some dinner at the mess. That ok with you?"

"Yeah. Sounds good. McKay?" Sheppard paused as the departing scientist turned to look at him. "Thanks."

"Yes, well…what are friends for?" McKay replied as he walked through the doors of Sheppard's quarters.

-oOo-

As Sheppard had hoped, four days later and he was back on active duty. Beckett and Heightmeyer were thrilled at his progress, they'd told him. Of course they hadn't realised he was still suffering headaches, and still hearing the Wraith queen's ever-dulcet tones. Still, he rationalised, what they didn't know wouldn't hurt them. All Sheppard needed now was to be allowed off world. Beckett had told him he was not cleared to fly yet, because of the headaches, even though the doctor believed they had improved. He also wouldn't okay 'gate travel. Sheppard was still working on that one. Which brought him to where he was heading - Weir's office.

Sheppard stood in the doorway of her office and smiled, what he hoped was his most charming smile at the leader of Atlantis.

Weir looked up from her laptop. "John. You're looking better. I hear Carson has cleared you for limited active duty."

"Yeah. That's what I've come to see you about." Sheppard tentatively said.

Weir looked ruefully at Sheppard. "Why am I not surprised? Before you spend the next fifteen minutes alternately whining, begging, moaning, and plastering the 'John Sheppard lost puppy dog' face on. Don't bother."

Sheppard instantly felt deflated, and he realised that must have shown on his face as Weir started to laugh.

"We know you too well, John! Carson, Kate and I have decided you can go off world."

Sheppard suddenly felt shocked, had she really said yes, before he'd even asked?

"But - and it's a big but, there are certain conditions. Lorne is leading a mission to S6Q- 526 tomorrow morning. The rest of your team is going. It's a simple recon mission, and there's no sentient life there. You will not be in command of the mission, you will not carry any weapon other than a hand stunner, _and_ Beckett will accompany you everywhere. I know this all sounds draconian, but we all have your best interests at heart." Weir looked up at Sheppard, and he thought she was waiting for him to complain. He really enjoyed surprising people, he decided.

"Yeah? Sounds great. Thanks." As he saw the astonished look on Weir's face, he decided he definitely liked surprising Weir.

She composed herself before replying, "Good. Get a good night's sleep. And I'll see you before you leave tomorrow. The mission briefing is scheduled for 0800 hours. John?"

Sheppard looked back at Weir as he started to leave her office. "Yeah?"

"It's good to have you back."

"Thanks. It's good to be back. 'Night Elizabeth."

Sheppard walked with an invigoured spring to his steps as he returned to his quarters. Tomorrow he would go off world, escape the team and gate to M3T-341, the planet where he believed Ford was hiding. Once he found his former lieutenant, and brought him back to Atlantis, everything would finally be back to normal.

Tbc.


	4. Chapter 4

Chapter 4.

_Thanks to Kodiak and Merlin for their beta skills and support. Thanks as well for the lovely reviews, they make writing even more of a pleasure! All mistakes are my own._

The briefing for the mission to S6Q-526 had gone just as Sheppard had expected - smoothly. He'd been left with little doubt that he was just an observer on this little trip, out for a little R and R. That was fine by him. He just needed to distract everyone, and gate off to find Ford. He'd taken the last of his migraine relieving medication the night before, and knew that if he had a bad headache on the mission, he wouldn't be able to hide it. Then again, once he found Ford he knew he'd be okay again anyway. He was positive of that. Who cared what Beckett, Weir or anyone else thought? He knew, and that's all that mattered, reasoned Sheppard.

He stood in front of the gate with Lorne and the rest of the team. Caldwell had insisted two of his men accompany them on the mission, and Sheppard was under no illusion that Caldwell trusted him. They were waiting for Beckett to arrive, and he was uncharacteristically late. Sheppard was starting to feel anxious and fidgety, and had a horrible feeling the mission was going to be cancelled. When Weir arrived a few minutes later, his fears were allayed.

"Unfortunately, Carson has been detained in the infirmary, a marine has broken his leg, so he won't be able to come. However, after discussing it with Carson, we feel the mission should go ahead. Rodney?" McKay looked up from the spot he was studying on the floor of the 'gate room. "Carson has asked that you take his place and stay with Colonel Sheppard at all times, since he can't spare anybody else."

"Great. I get to play babysitter. Thank you _so_ much," he grouched.

Sheppard walked up to McKay, grinning. "I promise not to pee my pants, mom."

McKay snorted. "Yes, very amusing. Just stay out of trouble, okay?"

"That's good coming from you. You sure you wouldn't like to put me on a leash?" Sheppard asked sarcastically.

"Sounds like a good idea, but I'm not enjoying the mental picture I'm getting."

"McKay, I never want to hear again that you're seeing pictures of me in your head – _eve_r," Sheppard retorted, smirking at his friend.

McKay walked off, huffing, "Ha, ha. Why do I get the feeling this mission is going to be disastrous?"

Weir frowned, before continuing. "Alright everybody. Check in is at 1600 hours. And John? Behave yourself."

Sheppard raised his eyebrows and shrugged. He inwardly wondered if she had some inclination about his plan, but quickly dismissed the idea. She wouldn't be letting him go if she did.

-oOo-

An hour later and Sheppard was starting to feel the beginnings of a headache. He had surreptitiously downed a couple of Tylenol several minutes before, and was hoping that would buy him some time before he made his dash for freedom. That was proving to be a little difficult with McKay playing nursemaid and guard dog rolled into one. Teyla, Ronon, Lorne and a couple of scientists had headed off in the opposite direction, which Sheppard was relieved about; escaping Ronon and Teyla would have been virtually impossible.

"You know, I have a hundred things I should be doing at the moment. I was in the middle of translating and de-ciphering the readings from the Ancient artifact you touched the other day. I'd made some progress before we left." He looked at Sheppard to see if he was paying attention, and satisfied that he was, continued, "It's a medical device and oddly enough it scanned you, though what it found I haven't figured out yet. I've left Zelenka to work on it, and he's going to get Carson to have a look at the data, not that he will be any help…"

Sheppard half- listened to McKay's ramblings, hoping he was nodding and grunting in the right places. His headache wasn't abating and he was becoming increasingly frustrated that he hadn't had an opportunity to escape McKay and the two marine's Caldwell had assigned to the team. Sheppard didn't want to hurt anyone, especially not McKay, and though his hand stunner could probably take out McKay and one marine, he knew he couldn't disable all three. Not without getting himself shot, anyway.

As often happened, fate had a hand in helping Sheppard achieve his goal. Walking with a throbbing head was proving difficult, and he stumbled, falling awkwardly on the ground. The two marines ran forward, McKay being in front, muttering away, and not noticing what had transpired behind him.

Sheppard took advantage of his misfortune immediately, stunning the two soldiers before they were anywhere near him, taking one of the men's P90's as he ran by. He then made a run for it, knowing McKay would never try to shoot him with his 9 mil. As Sheppard ran back towards the 'gate he heard McKay screaming at him to stop, and then heard his footsteps behind in pursuit. He also heard the scientist contacting Lorne over the radio, and knew he really had to move quickly to get back to the 'gate before Ronon got hold of him.

He was about a hundred feet from the 'gate when he heard McKay behind him. Running to the DHD, Sheppard dialled quickly, then ran towards the event horizon.

"Sheppard! Wait. What the hell are you doing?" a breathless McKay asked.

Sheppard briefly turned round, stunner in his hand. "I'm doing what I should have been allowed to do. Don't try and stop me. For what it's worth, I'm sorry." Sheppard then took the stunner and fired at McKay, the scientist immediately falling to the ground, unconscious.

Sheppard then sprinted for the 'gate, running through without looking back.

-oOo-

M3T-341 was just like any other planet in the Pegasus Galaxy: lush, green and wooded.

Sheppard trudged through the woodland looking for signs of his erstwhile Lieutenant. He'd been walking for about fifteen minutes and had seen no sign of him. He was certain Ford had flown a dart there. How, he had no idea, it was just a feeling, but a strong one.

As he approached a clearing, Sheppard noticed scorched scrubland ahead, and was elated to be able to make out the wreckage of a Wraith dart. Despite his pounding head, he ran to the dart as fast as his weary body would let him.

Going against every bit of military training he'd ever had, he called out Ford's name, somehow knowing it was Ford that had crashed the dart and not a Wraith. Sheppard was rewarded with silence. He approached the dart, and was relieved to find no body in the debris. There were, however, signs of someone leaving the wreckage, there still being footprints in the damp soil.

"Ford! It's John. I'm here to take you back to Atlantis with me, and everything's going to be fine. Ford!" Sheppard shouted on the top of his voice, desperate to attract the attention of the man he somehow knew was hiding here.

Sheppard kept calling, and after ten minutes started to move away from the dart towards the edge of the large scrubland area, intending to search the woods on the other side. It was possible Ford had been injured and needed help, and that's why he hadn't responded.

Walking through the dense woodland, Sheppard heard a twig snapping behind him, and spun around, P90 at the ready. The face staring at him, no, snarling at him, was sweaty, bruised, and thinner than Sheppard remembered. It was Ford.

"Well, look what the cat dragged in. I knew you'd come looking for me here, Sheppard. You look worse than I feel."

Sheppard sighed in relief. "Ford! Am I glad to see you. I knew you were here. Look, I know we've had our differences, but I want you to come back to Atlantis with me. Beckett can wean you off the enzyme, and things can go back to how they were. What do you say, buddy?"

Ford laughed maniacally. "You're kidding me, aren't you, Sheppard. No? How stupid do you think I am?"

"I don't think you're stupid. I know you're not. I just want…need you to come back with me. I want you back on my team. We could use your experience," implored Sheppard.

"You're an idiot, Sheppard. To think I used to look up to you! You don't get it, do you? Even McKay understands me better than you do. I don't want to come back. I like who I am now. I don't want to stop taking the enzyme. I like what I do, beating the Wraith at their own game." Ford snarled at Sheppard, and the colonel was taken aback at the younger man's hostility towards him.

Sheppard's shoulders sagged, his head pounding more viciously with every second. He wanted to lie down, and for the pain to just go away. "You don't mean that. I understand what you're going through and I can help. But I need you to come with me, willingly. I don't want to have to force you to come back to Atlantis. Please don't make me do that, " Sheppard begged.

Ford howled with laughter. "You don't want to have to force me?" Ford dissolved into hysteria again. He coughed before continuing, "You really are full of shit, Sheppard. Have you had a look at yourself in the mirror lately? You can barely hold your P90 up, let alone make me do anything." Ford cocked his own weapon at Sheppard, a Genii weapon, the pilot noted hollowly.

"Give me one reason why I shouldn't just shoot you? You've done nothing but undermine me! You think I've waited here to be friends again? I've waited here to kill you. I've lost my men, and you've ruined everything. I hate you, and you're going to pay for what you've done." Ford poked Sheppard in the chest with the gun. "Get moving, we're heading back to the gate. But first," Ford unclipped Sheppard's P90 and snatched it from Sheppard's hands, and then reached and took the stunner from his thigh strap, "I think I'll take those."

Sheppard looked at Ford in disbelief. What the hell was wrong with Ford? This was not what he'd thought would happen. He was beginning to realise he'd completely misjudged the long-term effects the enzyme had had on Ford.

"Listen, Ford - buddy. Let's sit down and talk about this. You're right, I'm not too good at the moment, and neither are you. Let's not do anything either of us will regret, okay?" Sheppard tried to reason with Ford.

Ford poked Sheppard again in the chest. "Shut up and get moving. There's something I have to do before I kill you."

-oOo-

McKay returned to consciousness slowly and miserably. He clumsily tapped his earpiece and called again for Lorne, with slurred speech, trying to tell the major what had happened. What seemed like an eternity later, Lorne's group ran towards the scientist, the major running over to McKay and helping him to sit up.

"McKay, what the hell happened? Where's the colonel and Caldwell's men?"

"Sheppard…went through 'gate. Men are back there…maybe quarter of a mile, not sure," McKay managed to slur.

Teyla knelt by McKay, her eyes full of concern. "Rodney, are you alright?"

McKay groaned. "Sheppard stunned me. He left through the gate. He's gone to find Ford." With every second McKay was becoming more lucid.

Ronon grunted. "I knew he'd try this. I should have stayed with him."

Lorne sighed. "It doesn't matter now, Ronon. Did you see the address he dialled?"

"Yes, not that it matters. I know where he's gone anyway," McKay wearily answered.

Lorne nodded. "Ronon, Teyla, go and bring back Caldwell's men. I'll dial Atlantis and fill them in on what's happened. We'll 'gate back and then Dr. Weir can decide what we do next."

McKay groaned again. "We go and get Sheppard back before he gets himself killed, that's what we'll do, Major."

"Of course we will, McKay." Lorne simply answered. "Of course we will."

-oOo-

Weir looked up from her paperwork to see Zelenka and Beckett purposefully running towards her office. Instinctively she knew something was very wrong.

"Dr. Zelenka, Carson. What's wrong?" She asked as calmly as she could. Deep down she knew the worry on the two men's faces had something to do with a certain Lt. Colonel.

"Dr. Weir. We have worrying news. I have managed to translate some of artifact's data, and what I have found is concerning," Zelenka's worried voice announced.

"You mean the artifact Colonel Sheppard activated?" Weir asked.

Beckett continued the dialogue, "Elizabeth, the artifact detected traces of a chemical in the colonel's brain." Beckett paused and ran a hand through his hair, before continuing. "I have no idea what the chemical is or does, but the fact that the device detected it, and that so much data has been emitted from it, is concerning, to say the least. Rodney could well be correct. The colonel's deterioration in health may not be a mental problem, but a physical one. As I have no idea at this point what the chemical has done to him, I think you should call him back to Atlantis immediately. Radek and I will continue to work on the translation, but I'd like the colonel to be near while we work on finishing this, just in case any more symptoms begin or return."

Weir sighed from frustration. "Okay. We'll dial the 'gate now, and call them back." She paused, frowning as she looked at Carson. "How serious could this be?"

Beckett considered Weir's question. "I have no idea. But I believe this could be very serious. Of course, it's also possible the chemical has worked it's way out of his brain and that he's fine. I don't want to take any chances though."

Weir opened her mouth to answer, but was interrupted by the sound of the 'gate activating and the tech sergeant calling out, "Unscheduled off world activation!"

She ran to the control room, Beckett and Zelenka on her heels. As she approached the sergeant she asked, "Is there an IDC?"

"Yes, ma'am. It's Major Lorne's team. Shall I lower the shield?"

Weir began to run down the stairs to the 'gate room, calling back her affirmation to the sergeant.

Lorne and the rest of the team exited the wormhole, and immediately Weir noticed Sheppard was not there.

"Major, where's Colonel Sheppard?" she anxiously enquired.

Before Lorne could answer, McKay angrily stomped forward. "He's gone off to find Ford. He stunned me, can you believe that? I knew something was still not right with him. Just wait till I get hold of him. I can't believe he'd actually stun me! Carson, when we find him, I want you to use that really giant needle you've got on him. My hands tingle and my head hurts, I might have permanent nerve damage…"

Beckett tutted. "Shut up, Rodney. You were stunned, stop whining like a wee lass. The situation is much more serious than you think."

McKay swallowed nervously. "What do you mean?"

Zelenka answered McKay's question. "I have translated more of artifact's data. Colonel Sheppard has an unidentified chemical in brain. Could be Wraith. Dr. Beckett has been helping with de-ciphering of information."

Beckett continued. "I don't know yet what the chemical is, or it's purpose, but my guess would be it has something to do with the Wraith queen's interrogation of the colonel." Beckett gestured at McKay, waving him forward. "Rodney, I need your help in translating and analysing the data."

"Of course. How bad could this be, Carson?"

Beckett started to walk briskly away, turning to answer the scientist, "Let's find out, shall we?" The doctor turned to Weir. "Elizabeth, I need the colonel in my infirmary now."

Weir nodded. "Okay. We'll find him." She turned to Lorne. "Major, do you know where he went?"

Lorne nodded in affirmation. "Yes, ma'am. M3T-341. Dr. McKay saw the 'gate address. Permission to take my team there now?"

"Permission granted, Major." Weir turned to Ronon and Teyla. "Bring him back to Atlantis."

Ronon nodded. "No problem. We'll have him here in no time"

Weir smiled worriedly. "Be careful, and good luck."

Just as the tech sergeant began to dial the address, the 'gates symbols came to life.

"Unscheduled off world activation," was shouted out for the second time that day.

Weir grimaced. "Raise the shield, sergeant."

"Yes, ma'am. I'm receiving a radio transmission," the sergeant calmly told Weir.

"Let's hear it," Weir replied.

The PA system in the control room crackled as the transmission began.

"Atlantis, this is Ford. Do you copy?"

Weir gasped. "Lieutenant, is that you?"

"Yes, ma'am. I have Colonel Sheppard here, and he's not looking too good." Ford replied.

Weir sighed in relief. "Thank God. Lieutenant, good job. Send him through. It will be good to see you again, Aiden." She turned to the tech sergeant. "Lower the shield."

Through the static of the radio transmission Weir was surprised to hear laughing.

"I don't think you quite understand the situation Dr. Weir. I'm not sending Sheppard through, and I'm not coming back. I want you to listen to what I have to say, and then I never want to see or hear from any of you again."

"Ford? What's going on?" Weir was beginning to feel a sense of foreboding, which made her blood turn to ice.

"Colonel Sheppard has caused the death of most of my men. His lack of faith in me, and his own actions have destroyed any credibility I had. He single-handedly sabotaged my mission to the Hive, and I wanted you to witness his punishment for his crimes."

Weir put her hand to her mouth in shock, before managing to compose herself.

"Aiden, I know things have been rough for you, but harming Colonel Sheppard will not change anything. He's very ill and needs urgent medical treatment. Let him through and you have my word we'll never bother you again. We won't continue to search for you, though that will hurt Colonel Sheppard more than you know."

"No. I don't believe you. You're all jealous of what I've become, and I'm ending this now. This is a warning to you. If you do try to capture me again, I will kill anyone who comes near me. Say goodbye to Colonel Sheppard, Dr. Weir."

Weir heard Sheppard's voice in the background, and then muffled shouts and grunts, and the sound of scuffling. Two shots rang out before the 'gate deactivated.

-oOo-

Sheppard stood by the 'gate. He was finding it hard to concentrate as his headache reached gargantuan proportions. His nausea had returned with a vengeance, and he was struggling not to throw up over his boots.

He watched as Ford dialled the 'gate.

"Ford. Talk to me. Whatever's bothering you - we can work it out. I'm not feeling so good. I'm going to sit, and we can talk, okay?"

Ford turned around, and for the first time Sheppard realised he had misjudged his former lieutenant. The hate on Ford's face was palpable, distorting the once handsome features, his personality twisted beyond recognition by the powerful drug.

"Shut up. I'm dialling Atlantis. I'm using you as an example to them. I'd like to be able to say I'm sorry, Sheppard. But I'm not." Ford gestured for Sheppard to stand in front of him as he snatched Sheppard's radio from his front vest pocket and started to talk into it.

Sheppard listened to Ford's words to Weir in shock. Ford intended to kill him as an example to others and as a means of punishing him. He suddenly realised what an error in judgement he'd made. Yet, his overriding concern was still for Ford, and he knew what he had to do.

With the little strength he had, he tackled a distracted Ford to the ground, knocking the Genii weapon from his hands.

Grabbing frantically for the weapon, he missed, but managed to roll away from Ford, grabbing the discarded P90 lying a few feet away. Sheppard scrambled dizzily to his feet aiming the weapon at Ford, just as Ford cocked the retrieved Genii rifle from the ground at Sheppard.

"Ford. Lower your weapon. My aim isn't too good at the moment, and I don't want to kill you. Don't make me do this. I need to think, and so do you. What do you say?" The P90 in Sheppard's hands wavered as he fought to control his shaking hands.

"I say get ready to die, Sheppard."

Ford's finger hesitated on the trigger giving Sheppard the time to aim his weapon at Ford's leg. He didn't hesitate, and fired a single shot into the former lieutenant's calf.

Ford screamed as the bullet tore through his flesh, and he pulled the trigger of his own weapon, hitting Sheppard in his left shoulder. Sheppard immediately fell to the ground as blood spattered his neck and face.

White-hot tendrils of agony coursed through Sheppard's shoulder and chest, and he gasped as he struggled to draw in a breath. He was aware of Ford running over to the DHD and disengaging the wormhole, before dialling out.

Sheppard then watched, through slitted eyes as Ford limped back over, standing over him. He gasped as Ford grabbed his vest, ripping it open as he studied Sheppard's wound, before grunting and releasing him.

"You'll bleed to death before they get here, Sheppard. I'd like to say it's been nice knowing you, but it hasn't. I consider your debt paid. I hope you rot in hell."

Sheppard's head now vied for first place in the sweepstakes of pain, and as darkness approached a single tear slid down his cheek as he watched Ford run through the gate.

Tbc.


	5. Chapter 5

Chapter 5.

_Well, here's Chapter 5. Thanks, as always to Merlin and Kodiak, my betas, inspirations, and great pals! All mistakes, unfortunately, are still all my own._

"Dial the planet!" Weir shouted at the top of her voice.

The tech sergeant immediately dialled the address, moments later shaking his head in frustration.

"I can't get a lock. Someone is dialling out."

Weir bit her lip. "Try again!" she ordered.

The sergeant re-dialled and this time the Stargate engaged. Lorne, Teyla and Ronon ran towards the event horizon, turning back to look for Weir's permission before embarking.

"Be careful. I'll have a medical team standing by. Good luck," Weir simply said.

"Yes, ma'am," Lorne replied, before gesturing for Ronon and Teyla to move out.

Weir tapped her radio as the 'gate shut off. "Medical team to the 'gate room," she calmly called into the radio, her hammering heart betraying her outward composure.

Beckett's voice came over the radio.

"Elizabeth? A team is on the way. What's going on?"

Weir responded to Beckett's question with a quiet, worried voice.

"We have reason to believe Colonel Sheppard has been injured. Hurry Carson, I have a really bad feeeling," she implored.

Beckett tutted. "On my way," he answered.

-oOo-

The team exited through the wormhole and immediately saw Sheppard lying a few feet from the 'gate. They ran over, while simultaneously scanning the area for any sign of Ford.

Teyla crouched down next to Sheppard, feeling his neck for a pulse.

"He is alive, but his pulse is very fast and weak," she declared.

She proceeded to check his body for wounds, instantly seeing the bloody mess underneath his vest. Removing a field dressing from her own vest pocket, she gingerly pulled back the fabric from Sheppard's jacket and t-shirt and pressed the dressing firmly into the wound. Sheppard moaned.

"John? You will be fine," she gently comforted her friend. "We will take care of you."

Sheppard struggled to open his eyes to slits. His shoulder burned, his head pounded, and nausea threatened to overwhelm him. Suddenly, he remembered what had happened.

Through gritted teeth he managed to whisper, "Ford?"

Ronon grunted a reply. "Gone. You hit him though. There's a trail of blood leading to the 'gate."

Sheppard closed his eyes. "He…left me…to die," he ground out through shallow breaths.

Teyla looked at Ronon. "Ronon, can you help me lift him? I need to see if there is an exit wound," she asked.

Ronon gently lifted Sheppard up from behind, as Teyla started to remove Sheppard's vest and jacket, which were both saturated with blood. Once she'd successfully removed them, she shuffled behind the colonel, ripping his t-shirt to expose a large wound, the size of a small fist. She quickly took another field dressing and firmly pressed it into the gory mess. Sheppard groaned in pain.

Teyla looked at Ronon in concern, before gazing at Lorne.

"Major?" she began, "his wounds are extremely serious. We need to return to Atlantis immediately," the Athosian worriedly reported.

Lorne moved round to look at the colonel, before nodding and tightly grimacing. "Okay, I'll go and dial the 'gate. Ronon?" Lorne looked at the Satedan, "Can you carry him to the 'gate?"

Ronon nodded. "No problem," he replied, as he gently lifted Sheppard into his arms, carrying the colonel while Teyla continued to press both wounds in Sheppard's shoulder as firmly as she could, as they slowly approached the event horizon.

"Atlantis, this is Lorne. Lower the shield, we're coming through. Dr. Weir?" Lorne paused waiting for a reply.

"Go ahead, Major," Weir replied nervously.

"I hope you've got that medical team on stand-by? We're going to need it," he gravely informed her.

"Understood. You're clear to come through," she stated.

-oOo-

As soon as the team exited through the gate, the medical team swarmed towards Sheppard. Ronon laid him carefully on the ground, placing Sheppard's head on Teyla's lap, and quickly moved out of the way as Teyla continued to put pressure on the bleeding wounds.

Beckett knelt above Sheppard quickly taking in the colonel's condition. "Christ, he's a mess. Okay, let's get an IV started," he ordered his team, as he lifted up the field dressing Teyla was holding down on the entry wound. Beckett continued, "Right, the entry wound isn't too good, let's look at the exit…" The doctor paused mid-sentence as Teyla lifted the dressing at the back of Sheppard's shoulder and Beckett looked behind the pilot to assess the wound.

He cursed under his breath. "Damn. I need some more pressure over here. Shelly?" Beckett called to his favourite nurse, "Can you take over from Teyla, love?"

The nurse took Teyla's place and the Athosian quietly moved out of the way, leaving the medical team to their work.

"Right," Beckett began, "Let's move him onto the gurney and get him to the infirmary. Melissa?" he called to his other trusted nurse, "Can you run ahead and pull four units of blood for me, and get prepped for surgery?"

The nurse nodded in affirmation, as she ran from the 'gate room towards the infirmary.

Sheppard quietly moaned as he was lifted onto the gurney. Beckett then placed an oxygen mask over the prone man's face, before looking down at the colonel and saying, "Don't worry, son. We'll get you sorted out in no time."

Beckett heard Sheppard mumble under the mask, and leant down to try and make out the colonel's slurred words. He lifted the mask as Sheppard whispered, "He…left me…to die…just…left me."

"It's okay, lad. We've got you now. Everything's going to be fine," he soothed as he replaced the oxygen mask.

Beckett turned to Weir and the others. "I need to get him into surgery immediately. He's lost a hell of a lot of blood and I need to stop the bleeding. I'll let you know when I have any news." Beckett then followed the gurney as it was rapidly pushed out of the doors and into the corridor.

Weir looked at the scene in front of her. Ronon and Teyla were covered in blood, as was the floor of the 'gate room. She eyed them, before asking, "Are you both ok?"

Teyla sadly nodded. "We are uninjured."

Weir smiled. "Good. Go and get cleaned up. It looks as though they're going have their hands full in the infirmary for the foreseeable future, but make sure you all get checked out when things have quietened down. Well done."

Weir turned to Lorne, who was standing quietly to the side of the group of people.

"Major? Any sign of Ford?" Weir asked.

Lorne shook his head. "No, ma'am. Colonel Sheppard hit him, but he dialled out before we arrived."

"Okay. We'll debrief at," Weir looked at her watch, "1800 hours. Dismissed."

The weary group headed off in different directions, but Weir stayed behind, lost in her thoughts as she surveyed the debris left by the medical team.

-oOo-

Running into the infirmary, McKay skidded to a halt as he took in the scene in front of him. Beckett was moving quickly and efficiently around Sheppard, barking orders at his team. A nurse was cutting away Sheppard's clothes, another hooking up blood to an IV. Beckett then moved on to insert more lines, as yet another nurse hooked the colonel up to a heart monitor.

McKay heard Beckett ask for more blood before the doctor muttered, "He's losing it faster than we can get it into him. Come on people, we need to stabilise him before we can get him into surgery."

Suddenly, McKay heard the heart monitor's alarms sounding, and he heard Beckett curse, gently scolding Sheppard. "Damn! Oh no you don't, Colonel. Stay with me. I need more blood. Shelly, let's squeeze it in. Let's get another line in with some more gelofusine, please," Beckett called to his nurse.

The nurse squeezed the bag of blood that led to the IV, as another put a third canular into Sheppard, his left forearm this time, quickly hooking up a bag of clear fluid. The heart monitor's alarms suddenly ceased.

"Right, we've done all we can here. Let's move him to surgery. Shelly?" Beckett called, "Can you pull another four units? If we're running short get Sophie to round up some donors."

The nurse nodded before replying, "We've only two more units, Doctor. I've already got Sophie rounding up suitable donors."

Beckett smiled. "Well done, lass."

McKay watched in bewildered silence as Beckett hustled past to scrub in, while two nurses pushed Sheppard's gurney towards the surgical suite.

"Carson?" the scientist called out.

Beckett briefly turned back towards McKay, before replying, "Not now, Rodney. I've got a battle on my hands. I'll let you know as soon as I have any news."

McKay watched as Beckett left, and as the enormity of the doctor's words sunk in, he silently did something he only seemed to do for a certain lieutenant colonel, he prayed.

-oOo-

Three hours later, and McKay was still waiting in the infirmary for news of Sheppard. Teyla and Ronon had joined him a couple of hours previously, and Elizabeth had been popping in and out regularly, as her responsibilities allowed.

Nurses had been scurrying in and out of the surgical suite over the last few hours, but all had avoided making eye contact with the anxious group of people camping out in the infirmary.

McKay got up from his chair, and started to pace nervously.

"Why haven't we heard anything yet?" He looked at his watch. "It's been over three hours. How long can it take to stitch up bullet wounds?" he asked no one in particular.

Teyla stood, and moved next to the frustrated scientist, placing a hand on McKay's arm to soothe him. "Rodney. The wound was very serious. It left a large hole in the back of Colonel Sheppard's shoulder. Give Dr. Beckett time to stop the bleeding and repair the damage."

McKay gulped as he took in Teyla's words, and was about to reply, when Beckett entered the infirmary, looking tired and sweaty. Before McKay could utter a word, Beckett held up his hands.

"Let's sit down over here and talk," he simply said.

Immediately, McKay returned to his seat, nervously wringing his hands together.

Beckett cleared his throat. "Right. I won't beat around the bush. Things didn't go too well, I'm afraid. Colonel Sheppard's wound is extremely serious. The bullet took half of his shoulder with it when it left him, causing massive blood loss and serious damage. I wasn't even able to close the larger wound, that's going to need a skin graft."

Beckett paused, taking in the worried faces of those around him. "He's alive, but in critical condition. We lost him twice on the table, and quite honestly we were lucky to get him back the second time. We'll be moving him into intensive care shortly, but I have to warn you…" Beckett paused again before sighing, "He may not survive the next few hours."

McKay looked at Beckett incredulously. "There must be something you can do, Carson. I know I've not always been complimentary about your voodoo skills, but honestly as far as doctors go, you're the best," he babbled at the doctor.

"Thank you, I think." Beckett tiredly rubbed his forehead, before continuing. "I've done all I can for him. You have to understand, he suffered a massive blood loss. The fact he held on as long as he did is a miracle. We're replacing the blood, and supporting him all we can. The rest is up to him."

"Can we see him?" McKay asked sadly.

Beckett grimaced, as he answered, "Not at the moment. We need to get him settled first. Give us half an hour and then you can - but only one at a time."

"Okay," McKay despondently replied.

-oOo-

Half an hour later Beckett led McKay to a curtained off area in the infirmary. He turned to McKay before entering. "Rodney, I should warn you, it's not pretty in there. Colonel Sheppard is hooked up to quite a few machines, including a ventilator."

McKay gulped, before quietly replying, "Okay."

As he entered the intensive care area, McKay was shocked at the sight before him. Sheppard lay on the bed, his naked body covered by a sheet and blankets. He was white as a ghost, and McKay thought there didn't seem to be any part of the man not attached to some piece of machinery or tubing. Sheppard's spiky, dark hair was a contrast to the deathly pallor of the man's skin, and McKay inwardly laughed that Sheppard's hair was still standing proud, despite the man's comatose state. McKay noticed the heavy bandaging on Sheppard's shoulder.

Beckett guided McKay to a chair by the side of Sheppard's bed. "Sit," he said simply to the unusually quiet scientist. "Now, I'll not be wanting you to stay here long. You'll just get in the way of my nurses, and I promised Elizabeth she can visit soon." Beckett took in the scientist's drawn and anxious face, and squeezed McKay's shoulder. "I know he looks pretty grim, Rodney. But he's made it this far, and that's something. If he gets through this, we've still got to sort out the problem with the chemical in his brain. So when you're done here, do you think you could carry on analysing the data with Radek?"

McKay looked up at Beckett, nodding. "Yes. Of course. Once he's over this, he's still going to need us to sort that out, isn't he?"

"Yes, he is." Beckett turned to the nurse who was fussing over various pieces of equipment. "Melissa, let me know if there's any change immediately," he asked the pretty curly haired woman.

She smiled, replying, "Of course, Doctor Beckett."

-oOo-

More than twenty-four hours later and Sheppard's condition remained stable, which Beckett assured everyone, was a relatively good sign.

McKay had, as promised, worked diligently on analysing the data from the artifact Sheppard had activated, and was now on his way to the infirmary to fill in Beckett on his findings, as well as checking on Sheppard.

On entering the infirmary, McKay went straight over to the curtained off area where Sheppard was. As he expected, Beckett was there writing down various readings from the monitors on a chart.

"Carson. How is he?" he enquired.

Beckett looked up from his notes. "Actually he's a little better. He's doing really well, considering. Have you got any news on the data from the device?"

McKay nodded. "Yes. Is it okay to talk here?"

"Let's go to my office. You can sit with him after, if you want to." Beckett moved away from Sheppard's bed and walked to his office, with McKay in tow.

Beckett sat behind his desk and looked expectantly at McKay.

"As we already knew, the device detected a chemical it didn't like when it scanned Sheppard's brain. The substance is Wraith. I've cross- referenced the data with the Ancient database and it appears the Wraith queen excretes a substance which takes up residence in the victim's brain."

Beckett interrupted McKay. "Aye, Kate said the colonel told her the queen ran her finger down his face, so that could be how it got in his bloodstream," the doctor hypothesised.

"Yes, that would make sense," McKay agreed. "The popular hypothesis by the Ancients, was that its purpose is to leave the victim open to suggestion, while causing a chemical imbalance in the brain, leaving the victim sick and confused, making him more liable to talk."

Beckett tutted. "Aye, that's a logical conclusion. Though why I didn't detect anything is surprising, to say the least."

"No, it's not. The only way to detect the chemical, once it's in the brain, is either by biopsy or scanning for the chemical. Since you didn't know about its existence, you couldn't scan for it," Mckay further explained.

"Fair enough. Anything else?" Beckett asked.

McKay paused before sighing. "Yes. Of the patients who had the enzyme in the brain, and there haven't been many recorded cases, most of them died pretty slowly and miserably. The enzyme started destroying the brains of the victims, resulting in irreversible and fatal brain damage."

Beckett took in McKay's words, before frowning. "So even if he gets through this, he's going to die a painful, slow death?" Beckett rose from his chair and wearily massaged the back of his neck. "Christ! This isn't fair. Why didn't I pick this up sooner?"

McKay interrupted Beckett, "Carson, there is a treatment. The artifact is also some sort of healing device. I haven't de-ciphered everything, but it can be used to heal the brain, though I don't know how – yet."

"That's encouraging news, Rodney. Any idea how long before the brain damage is irreversible?" Beckett needed to know the answer to that.

McKay nodded in affirmation. "Yes, about two weeks. So I figure Sheppard had his little encounter with the Wraith queen just over a week ago, that leaves us four or five days before his brain damage is irreversible. Will his present condition complicate things?"

Beckett sighed. "I have no idea, though if it's a gradual deterioration of the brain I would think that it's unlikely. How does he manage to get himself in these situations?" the doctor asked, exasperated.

McKay chuckled. "He certainly excels at getting into trouble, doesn't he?" McKay walked towards the door. "I'll check on him later. I need to get to work on researching the device. I'll let you know if I find anything more. Take care of him, Carson."

"Aye, that I will," the doctor answered, before walking off himself, to visit his most frequent patient, feeling a need to check on Sheppard in light of Rodney's news.

-oOo-

The next day passed slowly for McKay, and researching the artifact had resulted in little sleep for the scientist. He and Zelenka had worked round the clock to try and gather all the information they could. They had discovered how to use the medical device, but the stumbling block would be finding someone with a strong enough natural occurrence of the ATA gene to operate it. The most obvious candidate was the man who needed the treatment. The next strongest was Beckett, and McKay knew how much the doctor enjoyed activating Ancient technology.

Sheppard had remained in a coma, though McKay knew now that was due to sedation. He was still ventilated, but the last time McKay had spoken to Beckett, the doctor had been hopeful he could be weaned off the vent, if he continued to improve. A steady stream of visitors had been to see Sheppard, including his team and Weir, and McKay was now on his way to the infirmary to visit his friend and inform Beckett of his findings.

As he entered the infirmary, McKay was pleased to notice the privacy screens had been removed from Sheppard's bed. As he approached the pilot's bed, he saw Weir sitting there, quietly tapping on her palm pilot.

"Elizabeth. He's looking better, I think," McKay stated.

Weir looked up, a little startled by McKay's sudden words. "Yes, he is. Carson took him off the vent a couple of hours ago, and he seems to be coping really well, though he hasn't woken up yet. Carson isn't sure how he'll be when he wakes up. He may have deteriorated considerably mentally in the last couple of days." Weir paused, taking a deep breath before continuing, "Any luck with the device?"

McKay huffed. "Yes, but there are a couple of obstacles to overcome before we can use it. I need to find Carson. I'll be back."

Weir nodded as McKay went off in search of Beckett.

She looked across at Sheppard, immediately noticing his right hand twitching. Quickly moving towards the bed, Weir gently called to the colonel.

"John. Can you hear me? You're on Atlantis, and you're safe. Can you open your eyes for me?" she gently implored.

Sheppard opened his eyes and blinked in confusion.

"Hey. How are you feeling?" Weir asked, on seeing the man's open eyes.

When she received no reply, Weir gently stroked Sheppard's head.

"It's okay. You don't have to say anything. I need to get Carson though. I'll only be a minute," she explained. As she started to move away, Weir felt a hand on hers, and looking down saw that Sheppard had reached out to her.

"Ford…where's Ford?" Weir heard Sheppard whisper.

Weir smiled grimly at her military commander. "He's gone, John. He escaped. I'm so sorry I didn't listen to you. I was wrong. I hope you'll forgive me?" she gruffly asked, her voice breaking with emotion.

Sheppard swallowed before answering, "Got to…find him, 'Liz'beth. Let…me go."

"Of course you can search for him, but only when you're feeling better. I'll go and get Carson, now," she soothingly replied.

"'Kay," was all Sheppard could manage before closing his eyes.

Weir ran to Carson's office, entering without knocking. "Carson, John's awake!" she cried.

Beckett and McKay followed Weir back to Sheppard's bed, whose eyes were now closed, pain evident by the crease lines in his tense face.

"Colonel, are you in pain?" Beckett quietly asked.

Sheppard opened his eyes to slits, and Beckett struggled to comprehend the colonel's slurred words.

"I'm sorry, son. I can't hear what you're saying," Beckeet patiently told Sheppard.

"He…left me. Didn't listen…wanted me…dead," Sheppard whispered. The three people by Sheppard's bed all saw the devastation on the man's tortured face.

Weir took Sheppard's hand in hers, mindful of the IV's there. "John, shhh. It's going to be okay," she soothed. "Ford's not himself, you know that. When you're better, we'll find him and bring him back. Don't worry, just get some more rest. We'll find him. I promise."

Sheppard's breath hitched, as he answered Weir. "'Kay. I…knew he was…there."

"I know. You were right. I'm so sorry. Just…don't worry about anything, and get better," she gruffly replied, emotion threatening to take hold of her once again.

Beckett moved to the other side of Sheppard's bed and started to carry out various checks on his patient. Smiling grimly, he turned to McKay and Weir.

"Alright. Time to leave. I need to get him something for the pain he's obviously in. His shoulder is still bleeding a wee bit, and I need to redress it." Beckett turned to Rodney. "You can fill me in on your findings about the artifcat later. I need to get this sorted first." McKay nodded in affirmation before he and Weir walked away. "You've really gotten yourself in a mess this time, haven't you, son?" he asked the semi-conscious man in front of him.

Sheppard turned his head slightly to look at Beckett, mumbling a slurred, "Sorry," before closing his eyes.

Beckett reached over to a tray by Sheppard's bed and picked up a syringe, quickly emptying the contents into one of Sheppard's IV lines.

"What am I going to do with you?" he sighed before gently patting Sheppard's leg as he walked away from his most annoying patient. He knew he had a mammoth battle ahead of him, and for the second time Beckett wondered if his medical skills would be enough to save his friend from a painful and slow death.

Tbc.


	6. Chapter 6

Chapter six.

_Thanks for the reviews, they really inspire me to keep writing! Thanks to my betas, Merlin and Kodiak for their advice and hard work. All mistakes are my own._

Returning to consciousness was an extremely painful experience for Sheppard. The first thing he was aware of was noise. The beeping of a heart monitor, the mumbling of distant voices. Next, he was aware of the smell of antiseptic, combined with that indefinable infirmary smell. Finally, he opened his eyes, blinking furiously to try and see past the fog that was in front of them.

Sheppard then tried to remember exactly what had landed him in the infirmary this time. He began to remember snatches of what had happened. He'd run off to find Ford, and had found his former friend. As he struggled to recall what'd happened, vivid flashes of memory assaulted his confused brain. What had happened between Ford and him? He cried out a denial as an image of Ford standing over him, snarling, came into his head. An ache hit him, deep in his stomach, as the realisation hit that Ford had left him to die.

Sheppard had realised the enzyme had altered his former lieutenant, but was shocked when he remembered the look of pure hatred on the man's face. Venom directed squarely at him. At that moment, the pain in his shoulder suddenly woke up again. Fiery talons ripped viciously into him, along with the fiercest throbbing he thought he'd ever felt. His head was aching horribly, and he realised he felt short of breath and nauseous. Trying to compensate by breathing more deeply, he whimpered when breathing only made the pain worse.

His head really started to pound now, as the jackhammer started up again. He felt confused, alone and terrified. Bile rose in his oesophagus, and being unable to move, he gagged and vomited down the front of his sheets, choking as he tried to clear the acrid liquid from his airway.

Suddenly hands were on him, turning him onto his right side, and he felt relief as he stopped choking. Unfortunately, the simple act of moving him left Sheppard groaning hoarsely in agony. As the dry heaves stopped, he felt a cool cloth on his face, and felt the tubing from his nasal canular removed, and an oxygen mask placed over his face. He shivered as his sheets were pulled away from him, soon to be replaced with crisp new ones.

A soft voice spoke to him soothingly. "Easy now. It's okay, son. Try and take slow breaths. Don't try to breathe too deeply, it'll hurt if you do. That's it." Sheppard recognised the voice, but couldn't quite put a name to it. The voice continued, "You're in the infirmary. You've been injured, but you're going to be fine. I know you're in a lot of pain, and I've given you something for that, just be patient for a few minutes while it does its job."

Sheppard opened his eyes again to see someone standing over him. He groaned as the Wraith queen's voice started to echo in his head again, demanding he kneel.

Weakly, he managed to whisper, "No, not again…I…I can't do this …anymore. Just…kill me…please."

Sheppard felt a wave of pain envelop him and cried out again as his body stiffened and the air was squeezed out of his lungs. He felt himself arch up, but instead of panic, he felt relief, believing that he was dying. He gave up fighting, and surrendered himself to his fate.

-oOo-

As Beckett looked down at his patient, he felt sadness grip him. Sheppard was asleep again, but had suffered a serious seizure. He'd explained to Elizabeth, Rodney and the others the implications of Sheppard's condition, and had sent Rodney off to work on translating more of the database. Although they now knew how to operate the device, there still were many unanswered questions about any potential side-effects, and Beckett wanted to know more about any previous victims and the outcome of their treatments. Having those answers could potentially help Sheppard, and Beckett knew he needed all the help he could get.

Time was running out for his patient, of that Beckett was certain. He knew that the seizure was due to the chemical's attack on Sheppard's brain, and a C.A.T. scan had revealed brain damage this time. Beckett hoped it was reversible, but knew the longer Sheppard waited for treatment, the less chance he had of making a full recovery.

McKay's arrival interrupted Beckett from his thoughts.

"Carson? How's he holding up?" the scientist asked.

Beckett grimaced. "Not too well, I'm afraid. The seizure left some damage in its wake," he began. "Tell me you've got some good news. I don't know how much more of this he can take, Rodney," Beckett sighed.

McKay looked soberly down at Sheppard, before answering Beckett with a frustrated edge to his voice. "There's still too much to translate. I've got my entire team working on it, but it's so complicated, Carson. Honestly, I think we're way out of our depth on this one."

Beckett looked at McKay in alarm.

"Rodney, I don't need to tell you how important this is. It really is a matter of life and death this time. I really need to know more before we go ahead and try the device on him." Beckett stated, his voice heavy with emotion.

"Do you think I don't know that?" McKay answered angrily. "If Sheppard were awake now, he'd be telling me to pull myself together and just get on with it," he laughed bitterly. "He'd then tell me to stop whining and when I'd pulled yet another rabbit out of my hat, he'd pat me on the shoulder, smiling that irritating smirk of his, telling me he'd never stopped believing for one second that I'd succeed. I want him awake now, saying those things to me. Why did this have to happen, it's not fair!" Rodney posed the question, but they both knew it was rhetorical. Why had any of this happened? Ford, Sumner, Gall, Dumais...

Beckett looked at McKay sternly, knowing what he needed to do to motivate the distressed man. "Rodney, go back to your lab and find out how to save him. You're the only one who can do it. Colonel Sheppard believes in you, I know he does, so just do it, and don't come back until you have good news."

Beckett then turned his back on McKay and walked away from him, not looking back.

McKay took a step back in reaction to Beckett's words, before straightening himself up a little, and striding purposefully out of the infirmary towards his lab.

-oOo-

_The Wraith queen towered over her victim, shrieking in delight as she slowly drained the life from him. Sheppard cried out for Ford to move, to run away, as he sprayed bullets into the queen's back. But, Ford didn't move, he just screamed louder. Sheppard had no choice; he aimed for Ford's head and fired. He'd vowed never to do that again, after he'd been forced to kill Sumner, but his humanity demanded he take action. The marine collapsed to the floor, blood spraying in all directions as he fell backwards. As the queen hissed in annoyance, Sheppard fired endless rounds of bullets into her, until she fell to the floor, dead. He ran over to Ford, and shook his head in disbelief as the realisation of his actions sunk in. Without thinking, Sheppard pulled out his 9 mil, and put the gun to his temple, and pulled the trigger…_

Sheppard woke up shouting, his head dripping with sweat, and though the pain was ever present, this time that wasn't the cause of his fear. Another dream. He hoped that's what it was, prayed that's what it was. It had been so real though, he'd actually felt the bullet hit his temple, and he'd really wanted to die. What the hell was happening to him?

Cautiously opening his eyes, he went to rub them with his hands, only to find himself unable to move them. He turned his head to the side of him, and immediately understood the reason why – restraints, he was in restraints.

Focusing his eyes on his surroundings, Sheppard realised he was alone, and once again fear hit him. Why was he in restraints, and why was he alone? He remembered something about a young man, Ford? Was that his name? He couldn't remember. Nothing seemed to make sense anymore. He turned his head and noticed the thick bandage on his shoulder, and the IV lines in his arms, and tried to remember what had led to him being there. And where was he? Some sort of medical facility, he guessed, but was he a prisoner? Had he been injured while committing a crime? Sheppard wondered if he'd killed the man he kept seeing in his dreams, or had he killed the creature he saw in his head? Why was everything so fuzzy? He closed his eyes, suddenly feeling tired, and hoped everything would make sense when he woke up again.

-oOo-

The next twelve hours were spent with McKay frantically translating and analysing, and Beckett desperately trying to keep his patient reasonably comfortable. One had had some success; the other hadn't fared so well.

As McKay had managed to work out how to use the device, he had instructed Beckett in how to use it. Unfortunately, there was no way to test its effectiveness, so when Beckett used it on Sheppard it would be the first time it had been used in at least ten thousand years.

Beckett, in between learning about the artifact, had continued to care for his deteriorating patient. Sheppard had been slipping in and out of lucidity, and for an increasingly large part of his waking hours didn't know who anyone was. He appeared to be in horrific pain, and was suffering terrifying hallucinations, leaving him inconsolable at times. Beckett gathered they were to do with Ford, judging by Sheppard's tortured cries begging for Ford's life.

It was heartbreaking for the medical staff to witness Sheppard's decline. Beckett's two most experienced nurses twice had to wipe their eyes as their patient's plight temporarily overwhelmed them. Elizabeth had bravely continued to visit Sheppard, but Beckett witnessed the pain in her eyes at seeing her military commander reduced to a shadow of his former self.

Rodney had been conspicuous in his absence, though in all fairness, Beckett thought, McKay had been working tirelessly to research a cure for Sheppard. Beckett had briefed McKay about Sheppard's condition, but McKay had appeared to show little interest. Beckett thought it was probably a defence mechanism, and in all honestly didn't blame the scientist, he was doing all he could to help with Sheppard's predicament, while trying to get through it himself.

Beckett's musings were interrupted when McKay walked in to the infirmary.

"Carson, I've finally completed enough of the translation and analysis," McKay began. "I really think this will work. But – there's always a but, isn't there?" he observed, and smiled sadly, before continuing. "There is the serious possibility of a side-effect from using the device to heal the brain." He stopped and frowned, noticing Sheppard writhing in the bed a few feet away. McKay gulped as he realised Sheppard was now in restraints. Momentarily forgetting his previous train of thought, he looked at Beckett at snapped, "Are the restraints really necessary? Jesus, hasn't he gone through enough?"

Beckett cleared his throat. "I had no choice. None of the sedatives were working, and I can't risk giving him anything stronger than I already have. He was damaging his shoulder more by moving around so much, and when he tried to attack Melissa…" Beckett's voice suddenly cracked. Taking a moment to compose himself, he continued, "I have to consider the safety of my staff."

McKay nodded, feeling a little contrite for his outburst. "I'm sorry. I had no idea he was this bad." McKay nervously clenched his hands before continuing, "Anyway, where was I? Oh yes, the side-effect. There's no easy way to say this. The device, in repairing the damage and neutralising the Wraith chemical, can permanently erase the memories of the victim. And just so we're clear, I'm talking about Sheppard being cured, but never knowing anything about himself or anything he's ever learned, at all – ever again."

Beckett exhaled. " Bloody hell! Any idea on the likelihood of that happening?" he asked.

McKay grimaced. "Of the three patients that were in a similar position to Sheppard and had the device used on them, one died, one made a complete recovery, and one had her memory totally wiped. So that means he has thirty-three point three percent recurring chance of making a complete recovery, that's based on the limited information available."

Beckett nodded. "Okay, those odds aren't the greatest, but they're not the worst either. Shall we get on with it then?" he asked McKay.

McKay nodded gravely. "I think now is as good a time as any. I think I'd rather see him die than suffer like he is now," he added.

"Aye, me too," Beckett answered.

The two men approached Sheppard's bed, and Beckett nodded to Shelly, his favourite nurse. McKay handed Beckett the artifact and the doctor stood by Sheppard's head and closed his eyes in concentration. A low humming sound came from the device, and a bright, blue light enveloped Sheppard's body. Sheppard reacted by tensing, his body lifting off the bed.

As suddenly as the blue light appeared, it faded away. Beckett wavered, before opening his eyes.

"Are you okay?" McKay asked worriedly.

Beckett nodded. "Aye. That felt strange, though," he answered.

Both men looked down at Sheppard. The man's features were as pale as they were a few minutes earlier, but instead of tense lines and contorted, tortured features, he just lay there sleeping, his slack face looking peaceful for the first time.

"He's not dead, is he? Because he looks dead," McKay nervously asked Beckett.

Beckett frowned at the scientist. "Rodney, the heart monitor is still beeping! Of course he's not dead. He's just in a very deep sleep. I'll get another C.T. scan in a minute, and that should tell us whether we've sorted the problem out or not," he told McKay. "How long did you say it was before the patients regained consciousness?"

McKay sighed. "Days. Though the patient who didn't survive died the instant the treatment was given. So the fact that he's still here's a good sign, right?"

"I'd guess so. Let me get that scan organised and we'll know soon enough." Beckett paused, frowning. "Though, it may be days before we know if there's any memory loss, permanent or otherwise."

McKay smiled grimly. At least he was alive. "I know."

-oOo-

McKay and Weir sat in Beckett's office as Beckett patiently explained the results of Sheppard's latest battery of tests.

"Right. The good news. I'll give that to you first, as we bloody well need some," Beckett complained. "The C.T. scan shows the brain damage has completely been reversed. All the areas of the colonel's brain that had been affected are now good as new. Better, in fact."

Weir smiled broadly. "That's excellent news. Well done – to both of you," she looked at Beckett, then McKay.

Beckett nodded, and then continued, "As far as I can tell, the chemical has been eradicated, so he should make a full physical recovery."

McKay fidgeted impatiently. "Yes, yes. I think we all understood that. What's the bad news?"

"The scans of his brain are worrying me. It's too perfect," Beckett said matter-of-factly.

Weir's smile faltered. "How can it be 'too perfect'?" she asked.

"And so what if it is?" McKay added incredulously. "He's going to get better and now he's got a perfect brain – though I seriously doubt it's as good as mine," he added, stifling an indignant snort.

Beckett ignored McKay's comment. "The best way I can describe it to you, is that his brain looks like one would that hasn't been exposed to anything we encounter in life. It shows no flaws or imperfections, things that were there before, and had nothing to do with the Wraith queen's attack." Beckett paused for thought. "What I'm saying is, we all age, and the colonel's brain looks as if it hasn't. It's as if the device restored it to perfection, only it wasn't perfect to start with, none of our brains are."

McKay drummed his fingers annoyingly on arm of his chair.

"So?" he asked in a less than tolerant voice.

Beckett sighed. "So, I'm very concerned that all that's left is a brand new organ, filled with no memories or learned experiences. Like wiping a dirty slate clean."

Weir and McKay suddenly understood Beckett's concerns and both their faces showed their distress at learning Beckett's fears.

Weir was the first to talk. "I see. So, you believe he has lost his memories?" Beckett nodded in affirmation. "Will he know how to talk, walk and perform basic functions?"

Beckett shrugged. "I don't know. Though the patient who survived with no memories was normal in every way, except she didn't remember who she was, where she was, and in fact never remembered anything from her former life." The doctor grimaced, then brightened a little. "Though she did integrate back into her society, and found happiness, I don't underestimate how difficult that must have been."

"I see," Weir answered blankly, appearing to take in the information, but not react to it.

McKay huffed. "Well, he's alive. If he doesn't remember, we'll just have to re-educate him, won't we?"

"It's not as simple as that, Rodney." Beckett kindly explained.

Weir's gaze wandered from the hands in her lap to Beckett's face.

"Why not?" she asked exasperated.

Beckett let out a deep breath. "Elizabeth, if what I fear is in fact what has happened, he won't know any of us. Yes, he'll learn to know us, and Atlantis, but he'll more than likely never remember anything. None of his military training, how to fly a 'jumper, how to shoot a gun. He won't be able to continue as military commander here, and the SGC will want him returned to Earth, where he'll have no friends; nobody to look out for him, care for him. Do you see what the problem could be?"

McKay and Weir both simply nodded, not having the strength to answer the doctor.

Beckett got up from his chair and smiled sadly at his two friends. "Look, I'm not meaning to upset either of you. I may be wrong – Christ, I hope I am!" he started. "But – I thought I should warn you of my concerns. He's still alive, and that's an awful lot better than the alternative."

McKay was just starting to open his mouth to say something, when one of Beckett's nurses burst into the room, hovering in the doorway.

"Doctor Beckett. Colonel Sheppard is waking up. I thought you'd want to know immediately," the nurse informed those in the room.

The three occupants of Beckett's office ran into the infirmary, past the nurse and stopped at Sheppard's bed.

The man in question was blinking rapidly, as if trying to focus his eyes. Beckett leaned down over his patient, and touched Sheppard's arm with his hand.

"Colonel Sheppard? How are you feeling, son?" he asked calmly.

Sheppard didn't answer at first, and just stared into space.

Beckett tried again. "Colonel Sheppard. Can you look at me?"

Sheppard's head slowly turned towards Beckett's voice.

"That's good, lad. How are you feeling?" he asked again.

This time Sheppard answered, though his voice was hoarse and faint.

"Where am I?" he whispered.

"You're in the infirmary on Atlantis. Do you remember what happened?" Beckett asked, concern showing on his face.

"Infirmary? Atlantis? I don't understand," Sheppard's weak voice sounded confused and alarmed.

Beckett continued to talk to his patient calmly. "Yes. You've been injured, but are recovering nicely. You're safe and we've been taking care of you. Do you remember what happened?"

"No. Who are you?" Sheppard asked quietly.

"I'm Doctor Carson Beckett, your friend. Do you not remember, lad?" Beckett gently questioned the colonel.

"No. I don't know you, and I don't know what's happened. Please tell me what's going on." Sheppard was starting to panic.

Beckett patted Sheppard's arm reassuringly. "I know it's a little confusing, but I'll try and explain everything shortly. Can you tell me your name?" he asked gently.

Sheppard thought for a few seconds, a puzzled expression crossing his handsome features. When the answer to Beckett's question became apparent to Sheppard, his eyes widened in fear.

"No, no. I can't remember. Why can't I remember my name? Why am I here? Who are you?" Sheppard was starting to become agitated now.

Weir stepped forward into the line of Sheppard's sight.

"John? Calm down. I know this is frightening for you, but we'll explain everything to you, I promise."

Sheppard studied the woman in front of him, before asking, "Do I know you? You called me 'John', is that my name?"

"Yes, you do know me, my name is Elizabeth Weir. Your name is John Sheppard. Does any of that sound familiar to you?" Weir patiently asked, dreading the answer.

Sheppard's breath hitched as he answered, "No. I don't remember you, and I don't know who I am. Why can't I remember anything?" he pleaded like a small, lost child.

Beckett,once again patted the colonel's arm. "Don't worry lad, we'll explain everything. There's no need to worry at the moment. You've been very ill and you need time to get your bearings, that's all. All right?"

Sheppard weakly nodded his head, as his friends looked at him, fear and regret in their eyes.

Tbc.


	7. Chapter 7

Chapter 7.

_Well, here's the final chapter, folks! Thanks for all the great reviews. Thanks to Merlin, but especially Kodiak, who's had a really rough time with her computer and rushed this back to me! All mistakes are my own. _

Beckett entered his office and sighed as he took in the two solemn people sitting there, before clearing his throat to get their attention.

"He's sleeping now. I thought it kindest to sedate him. He was pretty upset, and not surprisingly so," Beckett informed McKay and Weir.

Rodney shifted his gaze from his lap to Beckett's face. "He's gone, isn't he? The Sheppard we knew is just…not there any more." Rodney's features were tense and pale.

Beckett grimaced, and blew out a tired breath. "I simply don't know. It appears he has no memories left intact. That doesn't necessarily mean they're gone for good, though. It's possible this is just temporary amnesia…" McKay looked up expectantly at the doctor. "But, before you get too hopeful, I have to say I think that's unlikely. Unfortunately, we don't have much basis for comparison." McKay's previously deflated look returned.

"I'm going to get Kate here to talk to the colonel tomorrow. She may be able to reassure and help him more than any of us can. It's going to be very hard on him, though." Beckett smiled grimly. "Let's not forget that he's alive. I know things look pretty bleak at the moment, but we have to stay positive for him. On the plus side, he's talking normally, so there's a good chance he may remember things his body has learned how to do without therapy. We'll just have to wait and see."

Weir hugged her arms around her chest in a pose Beckett knew well, and managed a brief smile in return for the news. "As you said, Carson, he's alive, and even if his present condition is permanent, that's a lot better than the alternative. We'll just have to focus on that, won't we?"

"I'm not giving up on him just yet. There's more data to translate and analyse on the Ancient device, and who knows, maybe I'll find something on restoring memories?" McKay chimed in.

Beckett nodded his head. "Good idea, Rodney. The colonel would never give up if he were in your position, and he'd be proud of you for trying," he said honestly.

"Yes, well… it's the least I can do." McKay faltered as his emotions started to get the better of him. Clearing his throat and sitting up straighter he continued, "Anyway, I'm going to head back to my lab now. I've got a long night ahead, don't I?" He paused again. "I'll be back later to sit with him. If he knows he has friends it may comfort him a little."

"That's a good idea, Rodney. Remember to eat and get some rest," Weir reminded him.

McKay nodded and rose from his chair, heading out of Beckett's office towards his lab.

Weir looked sadly at Beckett. "This is going to be very difficult to keep quiet. Caldwell is due to return in three weeks, and if John shows no sign of recovery before then, I'm going to have to inform the SGC."

"I know, lass. We've got three weeks to figure out what we can do, and I'm hopeful Rodney will pull that rabbit out of his hat once again," Beckett replied sadly, slouching against the door frame, letting his tiredness show outwardly.

Weir sighed, and stood. As she walked away, she turned back to look at Beckett. "If anyone can, Rodney can. Though you've performed quite a few miracles yourself recently, Carson," she complimented the doctor.

Beckett forced out a grateful smile, hoping they could perform a miracle this time – he knew only too well that's what it would take to restore the colonel to the man they all knew and loved.

-oOo-

Sheppard sat propped up in bed, staring into space. Though Dr. Beckett had explained the basics of his life to him- what his position was in Atlantis, and a brief outline of his personal details, he still didn't remember anything. He'd been given a palm pilot so he could write things down – his own, Beckett had told him, and he'd automatically known how to use it. He felt that was peculiar, to say the least. Sheppard knew he was a Lieutenant Colonel in the Air Force from a planet named Earth, and the commander of military operations on Atlantis, the city he was now in, which was in a different galaxy than Earth's. He didn't know whether that was a good thing or not. Instinctively he felt it was, but he also had an uneasy feeling that there was something nobody was telling him.

Sheppard was waiting for a woman named Kate Heightmeyer to come and talk to him. He'd been told she was a doctor who dealt with emotional and personal problems, as well as helping patients to remain mentally well. He was brought out of his thoughts by the arrival of a pretty, blonde haired woman, and John figured this was the lady in question.

"Colonel Sheppard? I'm Dr. Kate Heightmeyer. I know Carson, Dr. Beckett, has explained who I am and why I'm here. Before we start, is there anything you'd like to ask me?"

Sheppard scrutinised Heightmeyer's face, before finally asking, "Did I know you?"

Heightmeyer nodded, smiling. "Yes. We recently talked a fair amount. You can call me Kate, though you used to call me Doc," she laughed quietly, and Sheppard smiled politely at her, not understanding why she found that amusing.

"Now, Colonel, let's begin with how you're feeling at the moment," Heightmeyer began pleasantly.

"Would it be okay if you called me John?" Sheppard awkwardly asked. "It's just - I can't get my head around this Colonel stuff, and even though John doesn't seem familiar to me, I'm sort of used to that name now," he explained.

Heightmeyer nodded. "Of course. John is fine." She regarded Sheppard patiently for a few minutes, and when the colonel didn't answer, she realised he didn't know how these sessions worked.

"Col…John. You're supposed to answer my questions," the psychologist clarified.

Sheppard looked momentarily taken aback, but quickly hid his concern. "Uh, I feel okay. My shoulder's giving me hell, and I feel pretty tired. Dr. Beckett says I was seriously injured not long ago, but that I'm healing well."

Heightmeyer smiled encouragingly. "That's good. Are you in a lot of pain now? I can get Carson to give you something if you're uncomfortable."

"No, it's okay. He gave me something earlier and I didn't like the way it made me feel. It's only really bad if I try and move," Sheppard answered.

"Okay. I understand you've been told about yourself and your responsibilities here. Is there anything you want to talk about concerning those things?" Heightmeyer questioned the colonel.

Sheppard considered the psychologist's words. "Was I good at what I did? I mean, was I a good military man? Did my men like me…respect me? Have I been happy here?"

Heightmeyer put her hand on Sheppard's arm gently to interrupt him. "John. Slow down a minute." He looked across at her with a worried expression on his face, concerned he had somehow done or said something inappropriate.

Seeing the expression on his face, she quickly went to reassure the colonel. "It's okay, John. Everything's fine. If you want me to answer your questions you have to give me enough time to do that." She smiled warmly, but Sheppard still looked concerned.

"I'm sorry. I just feel – empty. I'm desperate to know who I am…to remember. I keep hoping something will suddenly make sense, something will just click and everything will fall into place." Sheppard knew he sounded desperate. "I've been asking the nurses questions all morning, but they either tell me to ask Dr. Beckett or not to worry. I have so many questions, and I need to know the answers."

Heightmeyer sighed. "This is a very difficult situation to be in, John. You must feel lonely, frustrated and scared," she began. "Those feelings are perfectly normal. But I think it's important you know that you have a very special place in everybody's heart here, and some very good friends. People who care very much about you, and who are going to help you through this. I want you to remember that. Will you do that for me?"

Sheppard mulled over Heightmeyer's words. "Sure. I can try. Tell me about myself. I mean tell me everything. I want to know about my life here – please," he begged.

"Of course. Where do I start?" Heightmeyer wondered out loud.

They two talked for over two hours, Heightmeyer answering Sheppard's questions as honestly as she felt appropriate, while gently reassuring him throughout their conversation. When she noticed the colonel's eyelids start to droop, she said goodbye and left him to sleep.

-oOo-

"Our session went well. Colonel Sheppard is understandably feeling isolated and apprehensive at the moment. He is, however, dealing with the situation incredibly well," Heightmeyer explained to the room of people in Weir's office.

"I've answered many of his questions, and he made some notes on his palm pilot of any salient points. When I spoke to him he was in a fair amount of pain, but very much like the old Colonel Sheppard, he refused painkillers. I believe this to be one of a few things of significance that I noticed," she explained.

Weir looked up from her own palm pilot. "How so?" she asked.

"Even though he has no memories, he is behaving as I would expect John Sheppard to, though he is much more open and unguarded in what he tells me. He obviously doesn't realise he loathes phychologists yet!" Hieghtmeyer laughed. "What I'm trying to say is - he isn't an empty shell. He's still the same person, with the same personality traits, and that's very encouraging."

McKay snorted. "How is that encouraging?"

Heightmeyer frowned before continuing. "It means that something has been left behind of him. He's not a blank canvas. It's just basic amnesia. That means even if his memory never fully returns, he'll be able to function here, even resume his role as military commander – eventually." Heightmeyer continued. "The colonel also understood all about being in the military, though he has no memory of himself being in the Air Force. He is familiar with the armed services, and when I talked about some of the missions he'd been on he was familiar with military terms, though again, he has no memory of the missions or the part he played in them."

"And that's good because?" McKay impatiently interrupted.

Heightmeyer smiled encouragingly. "That's good, because if he remembers military terms, he should remember how to fly, shoot a gun and things he usually does every day here – learned things, instinctual things. He knew how to use his palm pilot, for example. What I'm saying is that I'm hopeful we can re-educate him in who he is. The same old John Sheppard's still there."

Weir exhaled in relief. "That's very encouraging news, Kate. What's next for John?"

"We carry on talking to him, reassuring him. That's all we can do. I'd like to limit visitors to his team and you, of course. I don't want to overwhelm him." Heightmeyer explained.

Weir nodded, and turned to Beckett. "Carson, how's his physical health?"

"He's healing well. The skin graft I did a couple of days ago is doing well, though the damage to his shoulder is severe. He's going to need a lot of physical therapy, and possibly more surgery before he gets the full use back. Other than that he's extremely tired, which isn't surprising." Beckett answered.

Weir nodded. "Okay. I feel heartened by what I've just heard. Anything else?" she asked those in the room.

Ronon, who up till that point had been sitting quietly brooding in the background, stepped forward.

"Yeah. Has anybody explained to Sheppard how he got injured, why he can't remember anything, and about Ford?" he asked.

Weir looked uncomfortable for a minute. "I discussed this with Kate and Carson and after much thought, we've decided to keep Ford out of it for the moment. We haven't explained about the Wraith yet, or what happened on the Hive," she answered honestly.

"You're going to tell him though, aren't you?" Ronon asked.

"Of course we'll explain about the Wraith and the queen's interrogation. The situation with Ford… we're going to just keep to the basics. I'm going to ask you not to tell him about Ford shooting him, or Ford's anger towards him. He's got enough to deal with at the moment," Weir explained.

McKay looked at Weir incredulously. "You're going to tell him eventually, though?"

Weir grimaced. "If he doesn't remember – no. It'll be hard enough explaining about Ford's addiction to the enzyme without telling him his former second in command wanted to kill him. You didn't see him when he was brought through the 'gate. He was devastated. If I can protect him from that, I will."

"You can't be serious?" McKay asked, the pitch of his voice rising, as he became irritated.

"I assure you, I'm extremely serious," Weir answered calmly.

"He'd want to know. I know he would. You can't keep secrets from him, it's not fair," McKay simply said.

"Rodney, I understand what you're saying, but don't fight me on this," Weir sternly warned the scientist.

McKay didn't answer, and just walked out the conference room in annoyance.

"Right. I think we're done here," Weir announced.

Everyone left the room, with Weir staying behind tapping quietly on her palm pilot.

-oOo-

The next week passed slowly for Sheppard. The injury to his shoulder meant he'd been confined to the infirmary, in more pain than he'd wanted to admit. He'd started physical therapy on his shoulder the day before, and it had been hell, leaving him sweaty and spent, even though Beckett had insisted he receive pain relief.

He still hadn't remembered anything, though he was gradually becoming re-acquainted with his team and Weir. His sessions with Kate were going well and despite still feeling isolated and unnerved at times, he was slowly getting used to life in Atlantis. He was desperate to leave the infirmary and look around the city, and Beckett had said he would allow that very soon. McKay had told Sheppard that he had completed his analysis and translation on the healing device and found nothing more of use. Nor had he found anything on restoring lost memories, though McKay insisted he would continue searching as his responsibilities allowed.

McKay walking into the infirmary interrupted Sheppard's thoughts.

"Hey, Rodney," Sheppard called in greeting to the scientist.

"Colonel. You look…good. How are you today?"

Sheppard looked at McKay, puzzled. "I'm good. Why don't you call me John? Everybody else does. Except Ronon, he just calls me Sheppard, which somehow sounds right coming from him."

"I never have. I've always respected your rank, and that's what I usually call you, though sometimes I'll call you Sheppard, particularly when you annoy me," he answered.

"Do I annoy you a lot?" Sheppard wanted to know.

McKay snorted. "All the time."

Sheppard took in the scientist's words. "So, do we argue then? I thought we were friends?"

"We are friends. We merely enjoy the occasional argument, and you can be such an asshole at times," McKay replied, annoyance in his voice.

It was Sheppard's turn to show irritation. "And of course you'd never be an asshole, being a genius and all."

McKay stared at Sheppard, and the colonel looked at McKay in concern.

"Okay. I don't know where that came from. I…uh. Look, I didn't mean to be offensive, or anything," Sheppard said nervously.

"Yes, you did. You did mean to be offensive. Thank God!" McKay exclaimed.

Sheppard shook his head, perplexed at the scientist's words.

"Okay, you've lost me now. I've insulted you and that's somehow good?" he asked.

McKay grinned. "Yes, yes. It's good. You're still there! Don't you see?"

"Actually, no," Sheppard replied honestly.

"Over the last week you've been so polite, so formal. So…bland. This has proved to me you're in there somewhere, fighting to get out! By the way, how did you know I'm a genius?" McKay suddenly picked up on Sheppard's mention of his intelligence.

Sheppard considered McKay's question. "You've told me often enough, Rodney."

"No – I haven't. Every time I've visited you we've talked about you, your life here and that I'm a scientist, but I've never mentioned anything about my superior brain," McKay explained.

"That was very restrained of you. Can't ever seem to recall you being modest and unassuming before. You feeling okay?" Sheppard quipped, without thinking.

McKay glared at Sheppard before standing. "I'm going to get Carson. This is incredible!"

McKay ran off and returned a few seconds later with Beckett.

Sheppard searched the men's faces. "What's going on? What did I say?" he asked worriedly.

"You said, and I quote, 'I can't ever seem to recall you being modest and unassuming before.' You're remembering things!" McKay exclaimed jubilantly.

Beckett smiled broadly. "This is a very good sign. It could be possible that your memory is returning, slowly and in bits and pieces."

Sheppard shrugged, regretting it immediately when his shoulder reminded him of his injury.

"Damn. That hurt!" he yelped.

"Then I suggest you don't move it too much. Some things never change," Beckett chuckled as he walked off, leaving the men to talk.

-oOo-

That afternoon, McKay returned to the infirmary and approached Sheppard's bed and held out a pile of clothes.

"Here. Get dressed. Beckett said I can play mommy and take you out for a walk." McKay turned to leave, pulling the privacy screen as he went.

Five minutes later, when Sheppard hadn't emerged, McKay started to pace.

"For goodness sake, how long does it take to get changed! Sheppard, I would like to go sometime today!" he yelled.

A disembodied, muffled voice replied, "Relax, I'm having a little trouble getting my shirt on. Ow!"

McKay huffed. "Fine. Are you decent? What does it matter. Hang on, I'll help you."

After five more minutes of 'ouches', 'ow's' and 'damns', the two men had finally completed their task. One man was annoyed beyond belief, the other a little pale and sweaty from pain, cradling his left arm protectively in a sling.

"You okay? You look a little pale?" McKay asked.

Sheppard grimaced. "Yeah. Sorry about that. I'm still having trouble moving my arm. Come on, let's get out of here before Atilla changes his mind."

McKay chuckled and Sheppard gave him a searching look.

"You called Beckett Atilla. You used to do that when Beckett was being over-protective and playing mother hen. Your memory is definitely returning," McKay explained. "Come on. We're going to your quarters first, then to my lab."

-oOo-

Sheppard had been looking forward to seeing his quarters, and McKay waited in the doorway while Sheppard looked around, picking up various objects, including a picture of a man and a small dark-haired boy.

"Is this me?" Sheppard asked McKay.

McKay shrugged. "I have no idea, I've never been in your quarters before, only stood at the door." Sheppard beckoned for the scientist to enter, and handed him the framed photograph to look at.

"Looks like you, so I'm guessing it is. Sorry I can't help more. We may be friends, but you sort of keep your private life…well private," McKay explained.

Sheppard frowned. "Okay. Well nothing seems familiar here. But it does feel…nice. I feel comfortable – safe, here." He momentarily felt a rush of emotion, but quickly composed himself. "Right. Where to next?"

McKay walked towards the door. "My lab. You used to spend a lot of time there – usually annoying me. It may just jog your memory a bit."

"Lead the way," Sheppard said, smiling in anticipation.

-oOo-

On entering McKay 's lab, Sheppard had a feeling of déjà vu.

"I know this place," he simply said.

McKay grinned. "I thought it might seem familiar."

As Sheppard wandered around, he stared at a white board, where various mathematical equations were scrawled in black marker. He scrutinised a section of the board.

Pointing, he observed, "That's wrong."

McKay gazed at the numbers, before answering in an annoyed voice. "No, it's not. When did you suddenly become a math expert, anyway?"

Sheppard picked up a marker from the penholder underneath the board, and quickly wrote down a series of complicated calculations.

"See?" he asked the scientist. "That bit there. Whoever did this missed a zero, and then forgot to balance the equation."

McKay's mouth dropped open, and Sheppard stifled a laugh. "Leave that open and you'll catch flies with it." He abruptly stopped smiling, and he muttered quietly to himself, "My mom used to say that to me when I was a kid."

"How did you know that?" McKay demanded.

Sheppard went to shrug, then thinking better of it, simply answered, "In my file it said I was pretty good at math. It's not even difficult, Rodney. A kid could've worked that out."

"No. A kid couldn't have. That's advanced quantum mechanics. I was working on that before…before Ford… well, several weeks ago." McKay spluttered. "How can you do that?"

"In my personnel file it said I studied math at college. Can't think why I wouldn't have told you that." Sheppard frowned, not understanding why he would keep something like that from his friends.

McKay snorted. "Hah! I can. Never mind, the cat's out of the bag now, so to speak. Always suspected you were a geek in jock's clothing." McKay glared at Sheppard. "Which college did you go to?" he suddenly asked.

Sheppard paused, remembering what he'd read in his file. "Some place called M.I.T."

"What?" McKay guffawed.

"The Air Force gave me a scholarship apparently. Is that a good college?" Sheppard asked innocently.

McKay simply stared at the colonel. "Ah, it's not too bad," he lied, before wandering off muttering to himself.

As the two men wandered around the lab, Zelenka strolled in, and did a double take when spying Sheppard.

"I know you, don't I?" Sheppard asked the Czech. "You speak with an accent, I know your name. It's…it's…" Sheppard frowned in thought and then continued. "Z…Ze…Zelenka! I remembered!" Sheppard cried out.

Zelenka beamed. "Yes, Colonel. It is good to see you."

"Yeah, you too. I hope I'm not regularly offensive to you, too?" he asked the diminutive man.

"No. That is reserved for McKay only. He has special place in everyone's heart," Zelenka snickered.

Sheppard laughed for the first time since he'd woken up suffering from amnesia, and thought to himself how good that felt.

McKay touched Sheppard's arm to attract his attention. "We should head back to the infirmary now. It's getting late and you must be tired."

"Yeah, okay. Nice seeing you…Radek? Is that right?" Sheppard asked.

Zelenka pushed his glasses up his nose. "Yes, Colonel. Is good to see you well."

Sheppard grinned and followed McKay out of the lab, heading back towards the infirmary, feeling he was where he belonged - Atlantis.

-oOo-

Over the course of the next ten days, Sheppard's memories returned to him in fragments. Sometimes a familiar face would suddenly trigger a memory, sometimes a sentence uttered, other times just a sudden flash would appear in Sheppard's mind, and something else would fall in to place.

Along with the memories, came the nightmares. Sheppard had suffered his first one the second night he'd spent in his quarters. The dream was terrifying, and he'd run to the infirmary instinctively, finding Beckett there working. Beckett had calmed him down, and Sheppard had explained the frightening images he'd seen. When Sheppard talked of being tortured and witnessing other horrors, Beckett had patiently explained to Sheppard about his time in Afghanistan, having surmised that was what the dreams were about

Sheppard had carried on seeing Heightmeyer, who'd helped him come to terms again with some of the traumatic events he'd experienced. Nobody had mentioned about Ford having caused Sheppard's shoulder injury, and though Sheppard had no memories of the Wraith queen's interrogation, he had remembered about the disastrous mission with Ford to the Hive.

With his shoulder improving every day, and physical therapy going well, Sheppard had finally gained some useful movement in his arm, though Beckett insisted he not even think about sparring with Teyla or exercising.

He was on his way to see Weir about taking a trip to the Mainland, but decided to see Beckett first about the possibility of losing the sling, at least for part of the day. As he approached Beckett's office, he overheard raised voices and immediately recognised one as belonging to McKay. Deciding he wouldn't eavesdrop and would return later, he went to leave, but on hearing his name mentioned, lingered. As he strained to listen to the words being spoken, McKay's voice suddenly rose in pitch.

"You can't be serious, Elizabeth! This is so wrong. His memories have nearly all returned now. We have to tell him," McKay shouted out.

"No!" It was Weir's voice Sheppard heard next. "Listen to me, Rodney. He's been through too much. He remembers about Ford, and Kate told me he feels horrendous guilt and responsibility already. Telling him what Ford did would cause him unnecessary pain, and I want to protect him from that. If I can unburden him of that – I will."

"You're wrong, Elizabeth!" It was McKay again. "He deserves to know Ford tried to kill him and then left him for dead."

McKay's words struck as swiftly as a blade. Memories assaulted Sheppard's brain as he remembered his final encounter with Ford. Sheppard turned away from the office and ran. He ignored the pain in his shoulder, the fatigue in his body, and ran, flat out, only stopping when his body could go no further. He found himself on the outskirts of the city, on a balcony over-looking the beautiful ocean. It was raining, but Sheppard didn't care. He staggered over to the railing and collapsed against it, relishing the cold rain driving into his face. As emotion finally got the better of him he sank to his knees, sobbing. He pressed his face into the metal bars at the edge of the balcony, as tears ran down his face, mixing with the rivulets of water from the rain, washing away all the hurt and anger.

It was there that McKay found Sheppard some three hours later. When he hadn't arrived for his nightly check with Beckett, McKay had offered to find the absent colonel, after Beckett was preparing to call in Lorne to find his missing patient. McKay had stepped in, taking an LSD to hunt Sheppard down, figuring the man needed some time alone and that he could give him that.

Sheppard was lying on the floor of the balcony, curled in a ball, soaking wet and shivering, McKay immediately noticed. The scientist ran over to the prone form.

"Colonel? What the hell are you doing out here? It's freezing and you're soaking wet!" Seeing the colonel's drawn features and pale face, McKay knew something had happened.

"You heard, didn't you? And now you remember everything about Ford, don't you?" McKay asked.

Sheppard's voice quivered as he answered, "Yeah. I…I remember everything."

McKay sighed. "She should've told you. I told her to. God, I'm sorry you had to hear like that."

"S'okay. Really. Don't…don't worry about it. I had to find out sooner or later." Sheppard replied numbly.

"No. No, it's not okay. Elizabeth was wrong. But that doesn't matter anymore. You know now, that's the important thing." McKay reached down to turn Sheppard on his back, and shuffled behind him. "Come on, let's get you to the infirmary. Carson'll throw a fit when he sees the state you're in," he observed.

As McKay lifted Sheppard, the colonel groaned as his shoulder protested at the sudden movement, and started to waver.

"It's okay. I'll call Beckett and get him to send a gurney. Let's just get you inside and warm you up, all right?" McKay soothed.

Once inside, McKay didn't even attempt to remove the wet sling and jacket clinging to the shivering man. He helped Sheppard sink to the floor, and tapped his radio, contacting Beckett and filling him in on Sheppard's physical condition.

"M'Kay," Sheppard slurred. "Don't tell 'Liz'beth I know. Let me …protect her."

McKay sighed. "You haven't changed, have you? Always sacrificing yourself to protect others."

"She needs… protecting more than me… please, Rodney," Sheppard begged.

McKay looked at the pale face below him and seeing the plea on Sheppard's face, capitulated. "Okay, it's our secret - for now. You know you can always talk to me about this, right?"

"Yeah. Thanks." Sheppard whispered.

The arrival of a harassed and angry Beckett halted the conversation. Beckett's annoyance quickly changed to concern and compassion as he took in Sheppard's condition. McKay followed behind the gurney as Sheppard was wheeled quickly to the infirmary.

After an hour of anxious waiting, Beckett came out from behind the privacy screens shielding Sheppard, and smiled grimly. "He was a little hypothermic and has done his shoulder no good at all, but he'll be fine. He was a little confused, but either can't remember or isn't willing to discuss what triggered his little escapade. Did he say anything to you, Rodney?" Beckett asked.

McKay blankly stared at Beckett. "Rodney? Did the colonel say what had happened that made him sit in the rain?" the doctor asked again.

McKay jolted back to reality. "Ah, no. He said he'd remembered something painful, and needed to get away. Er, I think he said it was something to do with Afghanistan," he lied.

Beckett nodded grimly. "Okay. He's talked about that to me before. He had a pretty rough time, so it's understandable that it'd take time to come to terms with, if he ever had before." Beckett shook his head. "Poor lad, he's had a horrendous time."

Weir pursed her lips, before asking the question she was desperate to know the answer to. "Has this set him back, Carson?"

"I don't think so, Elizabeth. He's made such a dramatic improvement in the past few weeks, and he's bound to have some setbacks. I'll send Kate to speak to him tomorrow morning, and we'll see what she thinks," Beckett replied.

"Good. Let me know if anything changes. Good night gentlemen." Weir left the infirmary, turning back once to peer at the curtained off area of the infirmary.

"Can I speak to him?" McKay almost begged Beckett.

Beckett thought carefully, before answering, "Aye. Just for a few moments. I've got him hooked up to an IV, as he was dehydrated, and under a couple of warming blankets, but I think he'd welcome a friendly face."

McKay approached Sheppard's bed and closed the screen behind him. Sheppard drowsily opened his eyes.

"M'Kay," he whispered.

"Hey, how're you feeling?" the scientist asked.

Sheppard licked his lips. "Okay – tired, really tired. Listen – you won't tell Elizabeth will you?"

"No, I already promised. I won't let you down." McKay paused, and sighed before continuing, "Will you be okay? I mean it's pretty awful what happened, and I don't want you to suffer in silence, or anything. I'm here, anytime, if you need to talk."

"I know. Thanks." Sheppard answered quietly, and McKay noticed the glassy appearance of the colonel's eyes.

"I'd better go now. Carson said you need to sleep, so…I'll see you tomorrow?"

Sheppard bit his lower lip, and McKay felt uncomfortable witnessing his friend's battle to control his emotions.

Sheppard turned his head away from McKay and whispered softly, his voice wavering, "'Kay."

McKay started to walk away, but instinctively turned around as he pulled back the screen, he immediately noticed the repetitive quiver in Sheppard's right shoulder and heard the hitching of Sheppard's breathing and turned around and left, understanding his friend needed time alone.

Sheppard realised McKay had probably witnessed his emotional state, but knew the scientist wouldn't think lesser of him. As he drifted off into a restless slumber, for the second time in the last few weeks, a solitary tear slid down Sheppard's cheek, as the pain of Ford's betrayal haunted him. He decided there and then that he would find Ford, and return him to Atlantis, whatever the personal cost. He had never left a man behind, and he had no intention of starting now. He would find Ford and return him to the place they both belonged – Atlantis.

The end.


End file.
